Publications by authors named "Songnian Hu"

269 Publications

On the ultimate finishing line of the Human Genome Project.

Authors:
Jun Yu Songnian Hu

Innovation (N Y) 2021 Aug 12;2(3):100133. Epub 2021 Jun 12.

University of Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.1016/j.xinn.2021.100133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8454667PMC
August 2021

Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation.

Genomics Proteomics Bioinformatics 2021 Sep 3. Epub 2021 Sep 3.

Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China. Electronic address:

Baylisascaris schroederi, a roundworm (ascaridoid) parasite specific to the bamboo-feeding giant panda (Ailuropoda melanoleuca), represents a leading cause of mortality in wild populations. Here, we present a 293-Mb chromosome-level genome assembly of B. schroederi to infer its biology, including host adaptations. Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations, suggesting their potential for transmission and rapid adaptation to new hosts. Genomic and anatomical lines of evidence, including expansion and positive selection of genes related to the cuticle and basal metabolisms, indicated that B. schroederi undergoes specific adaptations to survive in the sharp-edged bamboo enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism. Additionally, we characterized the secretome of B. schroederi and predicted potential drug and vaccine targets for new control strategies. Overall, this genome resource provides new insights into the host adaptation of B. schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages. Our findings on B. schroederi's unique biology will also aid in the development of prevention and treatment methods to protect giant panda populations from roundworm parasitism.
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http://dx.doi.org/10.1016/j.gpb.2021.08.002DOI Listing
September 2021

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes.

Genomics Proteomics Bioinformatics 2021 Mar 16. Epub 2021 Mar 16.

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China. Electronic address:

Coding regions have complex interaction among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5'- to 3'- ends of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes but the decrease only starts from the ∼25 codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating universal selection for energy efficiency toward the N-terminus of encoded proteins. Within a genome, the decreasing GC gradient intensifies from lowly- to highly-expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradient at fourfold- and twofold- synonymous sites varied across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shaped the nucleotide sequences, especially efficient energy usage.
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http://dx.doi.org/10.1016/j.gpb.2021.03.002DOI Listing
March 2021

Evolutionary analysis and lineage designation of SARS-CoV-2 genomes.

Sci Bull (Beijing) 2021 Feb 6. Epub 2021 Feb 6.

State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.

The pandemic due to the SARS-CoV-2 virus, the etiological agent of Coronavirus Disease 2019 (COVID-19), has caused immense global disruption. With the rapid accumulation of SARS-CoV-2 genome sequences, however, thousands of genomic variants of SARS-CoV-2 are now publicly available. To improve the tracing of the viral genomes' evolution during the development of the pandemic, we analyzed single nucleotide variants (SNVs) in 121,618 high-quality SARS-CoV-2 genomes. We divided these viral genomes into two major lineages (L and S) based on variants at sites 8782 and 28144, and further divided the L lineage into two major sublineages (L1 and L2) using SNVs at sites 3037, 14408, and 23403. Subsequently, we categorized them into 130 sublineages (37 in S, 35 in L1, and 58 in L2) based on marker SNVs at 201 additional genomic sites. This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages. We also provide a companion website (www.covid19evolution.net) that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification. Finally, we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2's evolution. These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2's genome evolution.
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http://dx.doi.org/10.1016/j.scib.2021.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864783PMC
February 2021

Association of Gene Polymorphisms and Amlodipine-Induced Peripheral Edema in Chinese Han Patients with Essential Hypertension.

Pharmgenomics Pers Med 2021 2;14:189-197. Epub 2021 Feb 2.

Department of Pharmacy, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China.

Background: Amlodipine is one of the most used members of calcium channel blockers (CCB), available to treat hypertension. It is mainly metabolized by the Cytochrome P450 3A4/5 (CYP3A4/5) in the liver. Peripheral edema emerges as the major adverse drug reaction to amlodipine and is the primary reason for discontinuation of amlodipine therapy. However, genetic changes in may lead to changes in the tolerability of amlodipine.

Purpose: In this study, we were interested whether variants in CYP3A5 have a role to play in amlodipine-induced peripheral edema.

Methods: A total number of 240 Chinese Han patients that have experienced hypertension were included in the study. Sixty-four patients had experienced amlodipine-induced peripheral edema, while the remaining 176 patients with no history of edema formed the control group. Twenty-four single-nucleotide polymorphisms (SNPs) of gene were sequenced by targeted region sequencing method. The relationship of these genetic variants with amlodipine-induced peripheral edema risk was assessed using logistic regression.

Results: The allele frequencies of (rs15524), (rs4646453) and (rs776746) were significantly different between cases and controls (<0.05). The (CC) or (AA) carriers showed an increased risk of amlodipine-induced peripheral edema in dominant model. Meanwhile, patients carrying (AC/AA) showed a reduced risk of peripheral edema. Furthermore, we found a strong linkage disequilibrium among rs15524, rs4646453 and rs776746.

Conclusion: Our study reveals for the first time that and were associated with amlodipine-induced peripheral edema in Chinese Han patients with hypertension. However, further studies comprising larger number of samples, more related genes and other factors are wanted.
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http://dx.doi.org/10.2147/PGPM.S291277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7866951PMC
February 2021

A Method for Estimating 24-Hour Urinary Sodium Excretion by Casual Urine Specimen in Chinese Hypertensive Patients.

Am J Hypertens 2021 08;34(7):718-728

Institute of Hypertension, People's Hospital, Peking University, Beijing, China.

Background: High salt intake is a known risk factor of hypertension, which in turn increases the risk of stroke and cardiovascular diseases. The aim of this study was to develop and evaluate a method for predicting 24-hour urinary sodium excretion (UNa24h) using casual urine specimens in Chinese hypertensive patients.

Methods: A total of 966 patients with hypertension were included from 8 provinces across China. A UNa24h prediction model (Sun_C method) was developed for males and females using linear regression based on age, weight, sodium concentration in the spot urine (UNaspot), and creatinine concentration in the spot urine (UCrspot). The data were split into the training (70%) and testing (30%) sets to, respectively, develop and evaluate the Sun_C method.

Results: Compared with the Kawasaki, INTERSALT, and Tanaka methods, Sun_C method achieved a low and consistent mean bias (1.1 mmol/d) within the range from 106 to 212 mmol/d of UNa24h (equivalent to NaCl intake of 6-12 g/d). In addition, the Sun_C method showed no significant difference between the measured and estimated UNa24h in a paired t-test (P = 0.689). At individual level, Sun_C method had 79.8% of individuals at the cutoff under ±30% level.

Conclusions: Sun_C method may prove a reasonable method to estimate the daily dietary sodium intakes (particularly in the range of 6-12 g/d of NaCl) in Chinese hypertensive patients using spot urine measurements. As the amount of data increases in the future, the performance of our formulae will be further improved.
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http://dx.doi.org/10.1093/ajh/hpab020DOI Listing
August 2021

[Expert consensus on microbiome sequencing and analysis].

Sheng Wu Gong Cheng Xue Bao 2020 Dec;36(12):2516-2524

Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.
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http://dx.doi.org/10.13345/j.cjb.200386DOI Listing
December 2020

Complete sequences of two new KPC-harbouring plasmids in Klebsiella pneumoniae ST11 strains in China.

J Glob Antimicrob Resist 2021 03 13;24:114-120. Epub 2020 Dec 13.

Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China. Electronic address:

Objectives: Klebsiella pneumoniae carbapenemase (KPC) has spread across the world. The present study focused on exploring the sequences of two new KPC-harbouring plasmids in K. pneumoniae.

Methods: Eighteen KPC-harbouring K. pneumoniae isolates were collected from a tertiary teaching hospital in 2014 in Fujian, China, among which two new KPC-harbouring plasmids (pF77 and pF5) we identified. The characteristics of the plasmids and the isolates carrying them were investigated in detail.

Results: The two KPC-harbouring plasmids (pF5 and pF77) carried the antimicrobial resistance genes bla, bla, bla, catA2 and fosA3. Detailed sequence comparison revealed that the two plasmids might have evolved from recombination of the previously reported plasmids pKP1034 and pCT-KPC, which were considered to evolve from ancestor plasmids pHN7A8, pKPC-LK30 and pKPHS2. Plasmids pF5 and pF77 were non-conjugative and were mainly identified in sequence type 11 (ST11) K. pneumoniae isolates. Additionally, 4-55 core single nucleotide polymorphisms (SNPs) were identified in each pair of sequenced isolates that carried the identified plasmids.

Conclusion: Plasmids pF5 and pF77 as well as the previously reported plasmids pKP1034 and pCT-KPC were all detected in 2013-2014 in South China and were carried by ST11 K. pneumoniae isolates. SNP analysis indicated high similarity of the sequenced isolates. Therefore, spread of the group of plasmids may be due to an outbreak of clonal dissemination of ST11 KPC-producing K. pneumoniae. This study also highlights the importance of plasmid analysis in the surveillance and control of antibiotic resistance spread in clinical isolates.
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http://dx.doi.org/10.1016/j.jgar.2020.11.023DOI Listing
March 2021

A fine-scale map of genome-wide recombination in divergent Escherichia coli population.

Brief Bioinform 2021 Jul;22(4)

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.

Recombination is one of the most important molecular mechanisms of prokaryotic genome evolution, but its exact roles are still in debate. Here we try to infer genome-wide recombination within a species, utilizing a dataset of 149 complete genomes of Escherichia coli from diverse animal hosts and geographic origins, including 45 in-house sequenced with the single-molecular real-time platform. Two major clades identified based on physiological, clinical and ecological characteristics form distinct genetic lineages based on scarcity of interclade gene exchanges. By defining gene-based syntenies for genomic segments within and between the two clades, we build a fine-scale recombination map for this representative global E. coli population. The map suggests extensive within-clade recombination that often breaks physical linkages among individual genes but seldom interrupts the structure of genome organizational frameworks as well as primary metabolic portfolios supported by the framework integrity, possibly due to strong natural selection for both physiological compatibility and ecological fitness. In contrast, the between-clade recombination declines drastically when phylogenetic distance increases to the extent where a 10-fold reduction can be observed, establishing a firm genetic barrier between clades. Our empirical data suggest a critical role for such recombination events in the early stage of speciation where recombination rate is associated with phylogenetic distance in addition to sequence and gene variations. The extensive intraclade recombination binds sister strains into a quasisexual group and optimizes genes or alleles to streamline physiological activities, whereas the sharply declined interclade recombination split the population into clades adaptive to divergent ecological niches.
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http://dx.doi.org/10.1093/bib/bbaa335DOI Listing
July 2021

Identification of a mutation in a large Chinese family with atypical normokalemic periodic paralysis using whole-exome sequencing.

J Int Med Res 2020 Sep;48(9):300060520953643

Department of Neurology, the First Affiliated Hospital of Bengbu Medical College, Bengbu, China.

Objectives: Normokalemic periodic paralysis (NormoKPP) of skeletal muscle is an autosomal dominant disorder caused by mutations in the gene encoding voltage-gated sodium channel protein type 4 subunit alpha (), which leads to ion channel dysfunction. Little is known about the relationship between genotype and the clinical symptoms of NormoKPP. The present study aimed to evaluate the genetic variation in a large Chinese family with NormoKPP. The patients in this pedigree did not respond to saline treatment, but calcium gluconate treatment was effective.

Methods: We performed a series of clinical examinations and genetic analyses, using whole-exome and Sanger sequencing, to examine the mutation status of in a Chinese family segregating for NormoKPP.

Results: Whole-exome sequencing revealed a c.2111C>T substitution in in most of the affected family members. This mutation results in the amino acid substitution p.T704M.

Conclusions: These results support a causative role of this mutation in in NormoKPP, and provide information about the relationship between genotype and atypical clinical symptoms.
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http://dx.doi.org/10.1177/0300060520953643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7517994PMC
September 2020

Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China.

Protein Cell 2021 01;12(1):4-6

National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.

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http://dx.doi.org/10.1007/s13238-020-00772-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430935PMC
January 2021

Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia.

Front Microbiol 2020 24;11:1740. Epub 2020 Jul 24.

State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic MAGs, one MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.
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http://dx.doi.org/10.3389/fmicb.2020.01740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393216PMC
July 2020

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.

Genomics Proteomics Bioinformatics 2020 04 16;18(2):161-172. Epub 2020 Jul 16.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.
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http://dx.doi.org/10.1016/j.gpb.2018.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7646092PMC
April 2020

Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea.

Genomics Proteomics Bioinformatics 2020 06 17;18(3):341-351. Epub 2020 Jun 17.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative genomics and pathway analyses of Agaricales species. The draft, generated from both next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing platforms to overcome high genetic heterozygosity, is composed of a 56.5 Mb sequence and 15,384 predicted genes. This mushroom possesses a complex reproductive system, including tetrapolar heterothallic and secondary homothallic mechanisms, and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources. Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances, including B vitamins, unsaturated fatty acids, and N-acetylglucosamine. RNA-seq data show that A. cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage, whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis. These results reflect diverse functions of the two anatomical structures of the fruiting body. Our comprehensive genomic and transcriptomic data, as well as preliminary comparative analyses, provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
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http://dx.doi.org/10.1016/j.gpb.2018.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801210PMC
June 2020

Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in .

Int J Mol Sci 2020 Jun 13;21(12). Epub 2020 Jun 13.

CIRAD, UMR AGAP, F-34398 Montpellier, France.

The natural rubber biosynthetic pathway is well described in , although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of and loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.
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http://dx.doi.org/10.3390/ijms21124220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353026PMC
June 2020

A Reference Genome of Provides New Resources for Revealing Its Displacement by Pinewood Nematode.

Genes (Basel) 2020 05 19;11(5). Epub 2020 May 19.

State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

The , which was highly similar with in terms of morphological characteristics and biological properties-but had weaker pathogenicity to forests-was a native species often displaced by when occupying the same niche. Since the draft genome of the invasive has been published, the absence of a reference genome of still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of , including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between and . However, the losing of orphan genes and species-specific orthologous genes in may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in may jointly contribute to its displacement by . Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of , especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases.
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http://dx.doi.org/10.3390/genes11050570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288286PMC
May 2020

Post-transcriptional regulation of several biological processes involved in latex production in .

PeerJ 2020 29;8:e8932. Epub 2020 Apr 29.

CIRAD, UMR AGAP, Montpellier, France.

Background: Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in .

Methods: Genes producing microRNAs ( genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20-22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators.

Results: Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the and gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.
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http://dx.doi.org/10.7717/peerj.8932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195832PMC
April 2020

The genome evolution and domestication of tropical fruit mango.

Genome Biol 2020 03 6;21(1):60. Epub 2020 Mar 6.

Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.

Background: Mango is one of the world's most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis.

Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes.

Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.
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http://dx.doi.org/10.1186/s13059-020-01959-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059373PMC
March 2020

Semi-rational mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity.

Appl Microbiol Biotechnol 2020 Apr 24;104(8):3459-3471. Epub 2020 Feb 24.

Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Bioengineering, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Zone, Tianjin, 300457, China.

The biosynthesis of the valuable antibiotic enduracidin by Streptomyces fungicidicus TXX3120 is a complex multistep process. To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Comparative RNA-seq analysis indicated that the expression level of the endC gene during the enduracidin production phase was evidently lower than that of the other relevant genes to enduracidin biosynthesis. This result was further confirmed by quantitative RT-PCR, and the giant non-ribosomal peptide synthase (NRPS) encoded by endC was predicated to be the rate-limiting enzyme in enduracidin biosynthesis. To increase the expression of endC during the enduracidin production phase, a reporter-based selection system was developed by genetically replacing the initial part of the endC gene with a thiostrepton resistance gene (tsr), which will then act as a selectable marker to report the expression level of the rate-limiting gene endC, thereby facilitating the selection of enduracidin-overproducing mutants following random mutagenesis. After one round of mutagenesis, thiostrepton resistance selection, and restoration of the endC gene, three mutant strains with improved endC expression levels were obtained. Their highest enduracidin titers reached 9780.54, 9272.46, and 8849.06 U/mL, respectively representing 2.31-, 2.19-, and 2.09-fold of the initial industrial strain TXX3120. Our research provides a useful strategy for the rational breeding of industrial strains that synthesize complex natural products.
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http://dx.doi.org/10.1007/s00253-020-10488-0DOI Listing
April 2020

Gene family expansion of pinewood nematode to detoxify its host defence chemicals.

Mol Ecol 2020 03 17;29(5):940-955. Epub 2020 Feb 17.

State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

Gene gain/loss in the context of gene family dynamics plays an important role in evolutionary processes as organisms, particularly invasive species, adapt to new environments or niches. One notable example of this is the duplication of digestive proteases in some parasitic insects and helminths to meet nutritional requirements during animal parasitism. However, whether gene family expansion participates in the adaptation of a plant parasite nematode to its host remains unknown. Here, we compared the newly sequenced genomes of the pinewood nematode, Bursaphelenchus xylophilus, with the genomes of free-living, animal-parasitic and plant-parasitic nematodes. The results showed gene expansions occurring in 51 gene families in B. xylophilus, especially in xenobiotic detoxification pathways, including flavin monooxygenase (FMO), cytochrome P450 (CYP450), short chain dehydrogenase (SDR), alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), UDP-glucuronosyltransferase (UGT) and glutathione S-transferase (GST). Although a majority of these expansions probably resulted from gene duplications, nine ADH genes were potentially acquired by horizontal gene transfer (HGT) from fungi. From the transcriptomes of B. xylophilus treated with pine saplings and terpenes, candidate xenobiotic detoxification genes were identified. We propose that host defence chemicals led to gene family expansions of xenobiotic detoxification pathways in B. xylophilus facilitating its survival in pine resin ducts. This study contributes to a better understanding of how a parasitic nematode adapts to its host.
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http://dx.doi.org/10.1111/mec.15378DOI Listing
March 2020

5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease.

Clin Epigenetics 2020 01 21;12(1):17. Epub 2020 Jan 21.

State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China.

Background: The 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes. Its function has been studied extensively in tumors, neurodegenerative diseases, and atherosclerosis. Studies have reported that 5hmC modification is closely related to the phenotype transformation of vascular smooth muscle cells and endothelial dysfunction. However, its role in coronary artery disease (CAD) has not been fully studied.

Results: To investigate whether 5hmC modification correlates with CAD pathogenesis and whether 5hmC can be used as a biomarker, we used a low-input whole-genome sequencing technology based on selective chemical capture (hmC-Seal) to firstly generate the 5hmC profiles in the circulating cell-free DNA(cfDNA) of CAD patients, including stable coronary artery disease (sCAD) patients and acute myocardial infarction (AMI) patients. We detected a significant difference of 5hmC enrichment in gene bodies from CAD patients compared with normal coronary artery (NCA) individuals. Our results showed that CAD patients can be well separated from NCA individuals by 5hmC markers. The prediction performance of the model established by differentially regulated 5hmc modified genes were superior to common clinical indicators for the diagnosis of CAD (AUC = 0.93) and sCAD (AUC = 0.93). Specially, we found that 5hmC markers in cfDNA showed prediction potential for AMI (AUC = 0.95), which was superior to that of cardiac troponin I, muscle/brain creatine kinase, and myoglobin.

Conclusions: Our results suggest that 5hmC markers derived from cfDNA can serve as effective epigenetic biomarkers for minimally noninvasive diagnosis and prediction of CAD.
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http://dx.doi.org/10.1186/s13148-020-0810-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974971PMC
January 2020

The apricot ( L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis.

Hortic Res 2019 18;6:128. Epub 2019 Nov 18.

Beijing Academy of Forestry and Pomology Sciences, 100093 Beijing, PR China.

Apricots, scientifically known as L, are drupes that resemble and are closely related to peaches or plums. As one of the top consumed fruits, apricots are widely grown worldwide except in Antarctica. A high-quality reference genome for apricot is still unavailable, which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background, evolutionary diversity, and population diversity in apricot. DNA from was used to generate a standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on Sequel SMRT Cells, generating a total of 16.54 Gb of PacBio subreads (N50 = 13.55 kb). The high-quality reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70× coverage and 171× Illumina reads (40.46 Gb), combined with a genetic map for chromosome scaffolding. The assembled genome size was 221.9 Mb, with a contig NG50 size of 1.02 Mb. Scaffolds covering 92.88% of the assembled genome were anchored on eight chromosomes. Benchmarking Universal Single-Copy Orthologs analysis showed 98.0% complete genes. We predicted 30,436 protein-coding genes, and 38.28% of the genome was predicted to be repetitive. We found 981 contracted gene families, 1324 expanded gene families and 2300 apricot-specific genes. The differentially expressed gene (DEG) analysis indicated that a change in the expression of the 9--epoxycarotenoid dioxygenase () gene but not lycopene beta-cyclase (B) gene results in a low β-carotenoid content in the white cultivar "Dabaixing". This complete and highly contiguous reference genome will be of help for future studies of resistance to (PPV) and the identification and characterization of important agronomic genes and breeding strategies in apricot.
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http://dx.doi.org/10.1038/s41438-019-0215-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861294PMC
November 2019

Genomic and transcriptome identification of fluconazole-resistant genes for Trichosporon asahii.

Med Mycol 2020 Apr;58(3):393-400

Department of Dermatology, The Seventh Medical Center of PLA General Hospital (PLA Army General Hospital), Beijing 100700, China.

Trichosporon asahii infection is difficult to control clinically. This study identified a case with over 15 years of T. asahii infection-related systemic dissemination disease and conducted genome and transcriptome sequencing to identify fluconazole-resistant genes in fluconazole-resistant versus susceptible strains isolated from this patient's facial skin lesions. The data revealed mutations of the ergosterol biosynthetic pathway-related genes in the T. asahii genome of the fluconazole-resistant strain, that is, there were 36 novel mutations of the ERG11 gene, three point mutations (V458L, D457V, and D334S) in the ERG3, and a missense mutation (E349D) in ERG5 in the fluconazole-resistant strain of the T. asahii genome. To ensure that ERG11 is responsible for the fluconazole resistance, we thus simultaneously cultured the strains in vitro and cloned the ERG11 CDS sequences of both fluconazole-susceptible and -resistant strains into the Saccharomyces cerevisiae. These experiments confirmed that these mutations of ERG11 gene affected fluconazole resistance (> 64 μg/ml vs. <8 μg/ml of the MIC value between fluconazole-resistant and -susceptible strains) in Saccharomyces cerevisiae. In addition, expression of ergosterol biosynthesis pathway genes and drug transporter was upregulated in the fluconazole-resistant strain of T. asahii. Collectively, the fluconazole resistance in this female patient was associated with mutations of ERG11, ERG3, and ERG5 and the differential expression of drug transporter and fatty acid metabolic genes.
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http://dx.doi.org/10.1093/mmy/myz088DOI Listing
April 2020

Sequencing of Chinese castor lines reveals genetic signatures of selection and yield-associated loci.

Nat Commun 2019 07 31;10(1):3418. Epub 2019 Jul 31.

Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, Guangdong, China.

Oil produced by castor (Ricinus communis) has broad industrial applications. However, knowledge on the genetic diversity, especially genetic alterations that occurred during domestication and subsequent traits selection, of this oil crop is limited. Here, our population genomics analyses show that the Chinese castors have developed a geographic pattern, classified into the southern-, the middle-, and the northern-China groups. We detect a number of candidate genomic loci that are associated with the selection signals during the geographical differentiation and domestication. Using genome-wide association analysis, we identify candidate genes associated with nine agronomically important traits. One of the candidate genes encoding a glycosyltransferase related to cellulose and lignin biosynthesis is associated with both capsule dehiscence and endocarp thickness. We hypothesize that the abundance of cellulose or lignin in endocarp is an important factor for capsule dehiscence. Our results provide foundation for castor breeding and genetic study.
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http://dx.doi.org/10.1038/s41467-019-11228-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668449PMC
July 2019

Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.

Nucleic Acids Res 2019 07;47(W1):W270-W275

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China.

Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree formats, such as Newick/Phylip, Nexus, Nhx and PhyloXML, and provides a range of visualization options, using fifteen types of custom annotation datasets. The new version of Evolview was designed to provide simple tree uploads, manipulation and viewing options with additional annotation types. The 'dataset system' used for visualizing tree information has evolved substantially from the previous version, and the user can draw on a wide range of additional example visualizations. Developments since the last public release include a complete redesign of the user interface, new annotation dataset types, additional tree visualization styles, full-text search of the documentation, and some backend updates. The project management aspect of Evolview was also updated, with a unified approach to tree and project management and sharing. Evolview is freely available at: https://www.evolgenius.info/evolview/.
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http://dx.doi.org/10.1093/nar/gkz357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602473PMC
July 2019

Transcriptomic profiling reveals MEP pathway contributing to ginsenoside biosynthesis in Panax ginseng.

BMC Genomics 2019 May 17;20(1):383. Epub 2019 May 17.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.

Background: Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently. But their gene expression characteristics are still under reveal in P. ginseng. With the development of the high-throughput next generation sequencing (NGS) technologies, we have opportunities to discover more about the complex ginsenoside biosynthesis pathways in P. ginseng.

Results: We carried out deep RNA sequencing and comprehensive analyses on the ginseng root samples of 1-5 years old and five different tissues of 5 years old ginseng plants. The de novo assembly totally generated 48,165 unigenes, including 380 genes related to ginsenoside biosynthesis and all the genes encoding the enzymes of the MEP pathway and the MVA pathway. We further illustrated the gene expression profiles related to ginsenoside biosynthesis among 1-5 year-old roots and different tissues of 5 year-old ginseng plants. Particularly for the first time, we revealed that the gene transcript abundances of the MEP pathway were similar to those of the MVA pathway in ginseng roots but higher in ginseng leaves. The IspD was predicated to be the rate-limiting enzyme in the MEP pathway through both co-expression network and gene expression profile analyses.

Conclusions: At the transcriptional level, the MEP pathway has similar contribution to ginsenoside biosynthesis in ginseng roots, but much higher in ginseng leaves, compared with the MVA pathway. The IspD might be the key enzyme for ginsenoside generation through the MEP pathway. These results provide new information for further synthetic biology study on ginsenoside metabolic regulation.
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http://dx.doi.org/10.1186/s12864-019-5718-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524269PMC
May 2019

Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice.

Mol Plant 2019 08 3;12(8):1103-1113. Epub 2019 May 3.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored. However, the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves; at the post-transcriptional level, aging also modulated miR528 levels by enhancing pri-miR528 alternative splicing. We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties, which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528. Taken together, our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.
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http://dx.doi.org/10.1016/j.molp.2019.04.009DOI Listing
August 2019

Enhancement of oxidative stress contributes to increased pathogenicity of the invasive pine wood nematode.

Philos Trans R Soc Lond B Biol Sci 2019 03;374(1767):20180323

1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China.

Reactive oxygen species (ROS) play important roles in defence response of host plants versus pathogens. While generation and detoxification of ROS is well understood, how varied ability of different isolates of pathogens to overcome host ROS, or ROS contribution to a particular isolate's pathogenicity, remains largely unexplored. Here, we report that transcriptional regulation of the ROS pathway, in combination with the insulin pathway, increases the pathogenicity of invasive species Bursaphelenchus xylophilus. The results showed a positive correlation between fecundity and pathogenicity of different nematode isolates. The virulent isolates from introduced populations in Japan, China and Europe had significantly higher fecundity than native avirulent isolates from the USA. Increased expression of Mn-SOD and reduced expression of catalase/ GPX-5 and HO accumulation during invasion are associated with virulent strains. Additional HO could improve fecundity of Bu. xylophilus. Furthermore, depletion of Mn-SOD decreased fecundity and virulence of Bu. xylophilus, while the insulin pathway is significantly affected. Thus, we propose that destructive pathogenicity of Bu. xylophilus to pines is partly owing to upregulated fecundity modulated by the insulin pathway in association with the ROS pathway and further enhanced by HO oxidative stress. These findings provide a better understanding of pathogenic mechanisms in plant-pathogen interactions and adaptive evolution of invasive species. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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http://dx.doi.org/10.1098/rstb.2018.0323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367158PMC
March 2019

Genome-wide analysis in Hevea brasiliensis laticifers revealed species-specific post-transcriptional regulations of several redox-related genes.

Sci Rep 2019 04 5;9(1):5701. Epub 2019 Apr 5.

CIRAD, UMR AGAP, F-34398, Montpellier, France.

MicroRNA-mediated post-transcriptional regulation has been reported on ROS production and scavenging systems. Although microRNAs first appeared highly conserved among plant species, several aspects of biogenesis, function and evolution of microRNAs were shown to differ. High throughput transcriptome and degradome analyses enable to identify small RNAs and their mRNA targets. A non-photosynthetic tissue particularly prone to redox reactions, laticifers from Hevea brasiliensis, revealed species-specific post-transcriptional regulations. This paper sets out to identify the 407 genes of the thirty main redox-related gene families harboured by the Hevea genome. There are 161 redox-related genes expressed in latex. Thirteen of these redox-related genes were targeted by 11 microRNAs. To our knowledge, this is the first report on a mutation in the miR398 binding site of the cytosolic CuZnSOD. A working model was proposed for transcriptional and post-transcriptional regulation with respect to the predicted subcellular localization of deduced proteins.
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http://dx.doi.org/10.1038/s41598-019-42197-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450977PMC
April 2019

The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize.

Mol Plant 2019 03 23;12(3):402-409. Epub 2019 Feb 23.

Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China. Electronic address:

Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS-related lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.
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http://dx.doi.org/10.1016/j.molp.2019.02.009DOI Listing
March 2019
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