Publications by authors named "Xiao-Ru Wang"

112 Publications

Asthma treatment adherence and related factors in Shanghai, China.

Chin Med J (Engl) 2021 Sep 23. Epub 2021 Sep 23.

Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China Department of Respiratory and Critical Care Medicine, Ruijin Hospital Northern Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, China Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China Department of Respiratory Medicine, TongRen Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200050, China Department of Respiratory Medicine, Da Hua Hospital, Xuhui District, Shanghai 200237, China Department of Respiratory Medicine, Shanghai Sixth People's Hospital (Jinshan Branch), Shanghai 201500, China Department of Respiratory Medicine, People's Hospital of Shanghai Pudong District, Shanghai 201200, China Department of Xiao Gan, Shanghai Ninth People's Hospital (Huangpu Branch), Shanghai 200011, China Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University School of Medicine, Shanghai 200040, China Department of Respiratory Medicine, People's Hospital of Shanghai Qingpu District, Shanghai 201700, China.

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http://dx.doi.org/10.1097/CM9.0000000000001680DOI Listing
September 2021

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome.

Hortic Res 2021 Sep 1;8(1):177. Epub 2021 Sep 1.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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http://dx.doi.org/10.1038/s41438-021-00614-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8408255PMC
September 2021

Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger.

Hortic Res 2021 Aug 5;8(1):188. Epub 2021 Aug 5.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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http://dx.doi.org/10.1038/s41438-021-00599-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342452PMC
August 2021

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene.

Microorganisms 2021 Feb 11;9(2). Epub 2021 Feb 11.

Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden.

On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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http://dx.doi.org/10.3390/microorganisms9020355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916980PMC
February 2021

Divergent patterns between phenotypic and genetic variation in Scots pine.

Plant Commun 2021 Jan 29;2(1):100139. Epub 2020 Dec 29.

Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden.

In boreal forests, autumn frost tolerance in seedlings is a critical fitness component because it determines survival rates during regeneration. To understand the forces that drive local adaptation in this trait, we conducted freezing tests in a common garden setting for 54 (Scots pine) populations (>5000 seedlings) collected across Scandinavia into western Russia, and genotyped 24 of these populations (>900 seedlings) at >10 000 SNPs. Variation in cold hardiness among populations, as measured by , was above 80% and followed a distinct cline along latitude and longitude, demonstrating significant adaptation to climate at origin. In contrast, the genetic differentiation was very weak (mean 0.37%). Despite even allele frequency distribution in the vast majority of SNPs among all populations, a few rare alleles appeared at very high or at fixation in marginal populations restricted to northwestern Fennoscandia. Genotype-environment associations showed that climate variables explained 2.9% of the genetic differentiation, while genotype-phenotype associations revealed a high marker-estimated heritability of frost hardiness of 0.56, but identified no major loci. Very extensive gene flow, strong local adaptation, and signals of complex demographic history across markers are interesting topics of forthcoming studies on this species to better clarify signatures of selection and demography.
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http://dx.doi.org/10.1016/j.xplc.2020.100139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816077PMC
January 2021

UV-B-induced molecular mechanisms of stress physiology responses in the major northern Chinese conifer Pinus tabuliformis Carr.

Tree Physiol 2021 07;41(7):1247-1263

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 35 Qinghua E Rd, Beijing 100083, China.

During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer's response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.
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http://dx.doi.org/10.1093/treephys/tpaa180DOI Listing
July 2021

Chromosome-level genome assembly of a parent species of widely cultivated azaleas.

Nat Commun 2020 10 19;11(1):5269. Epub 2020 Oct 19.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China.

Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.
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http://dx.doi.org/10.1038/s41467-020-18771-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572368PMC
October 2020

Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.

Genome Biol Evol 2020 11;12(11):1965-1974

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.

Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.
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http://dx.doi.org/10.1093/gbe/evaa172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643612PMC
November 2020

Effects of landscapes and range expansion on population structure and local adaptation.

New Phytol 2020 10 18;228(1):330-343. Epub 2020 May 18.

Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China.

Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2-19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype-environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.
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http://dx.doi.org/10.1111/nph.16619DOI Listing
October 2020

Landscape genomics predicts climate change-related genetic offset for the widespread (Cupressaceae).

Evol Appl 2020 Apr 22;13(4):665-676. Epub 2019 Nov 22.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China.

Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for .
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http://dx.doi.org/10.1111/eva.12891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086053PMC
April 2020

Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing.

Heredity (Edinb) 2020 05 2;124(5):633-646. Epub 2020 Mar 2.

Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden.

Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.
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http://dx.doi.org/10.1038/s41437-020-0302-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171117PMC
May 2020

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants.

Genome Biol Evol 2020 01;12(1):3586-3598

Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Sweden.

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.
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http://dx.doi.org/10.1093/gbe/evz263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944214PMC
January 2020

Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for (Cupressaceae).

G3 (Bethesda) 2019 11 5;9(11):3663-3672. Epub 2019 Nov 5.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China,

is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species' genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species' 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.
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http://dx.doi.org/10.1534/g3.119.400684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829139PMC
November 2019

Numerical evaluation of ablation zone under different tip temperatures during radiofrequency ablation.

Math Biosci Eng 2019 03;16(4):2514-2531

College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.

The present study aimed at investigating the relationship between the shape and size of ablation zone and the ablation time during radiofrequency ablation (RFA) at different tip temperatures (80, 85, 90, and 95 °C). A two-dimensional simulation model of liver RFA using single-electrode was first built by finite element method (FEM). A closed-loop proportional-integral (PI) controller was employed in the FEM model. The heat transfer issues were solved based on Pennes biological equation. To improve simulation accuracy of the FEM models, temperature-dependent forms of the electrical conductivity and the thermal conductivity were adopted in the model. The ablation zone was assessed by 54 °C isothermal contour (IT54). The ablation zone sizes obtained from the numerical simulations and ex vivo experiments were compared to evaluate the validity of the numerical model. All the four tip temperatures (80, 85, 90, and 95 °C) were tested using 3 ex vivo porcine livers respectively. According to numerical simulation results, the characterization functions of the ablation volume and the ablative margin (AM) were derived. The proposed curve functions could precisely characterize the shape and size of ablation zone at different preset tip values, and the statistical results showed that the prediction curves had a good consistency with simulation curves. This paper proposed the prediction models of the ablation zone in the RFA process, which could be used to achieve accurate planning of RFA needle placements and optimize patient care during temperature-controlled RFA therapy.
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http://dx.doi.org/10.3934/mbe.2019126DOI Listing
March 2019

Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.

Gigascience 2019 02;8(2)

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Background: Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.

Findings: We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.

Conclusions: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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http://dx.doi.org/10.1093/gigascience/giy164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377399PMC
February 2019

De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.

Sci China Life Sci 2019 May 17;62(5):609-618. Epub 2019 Jan 17.

State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.
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http://dx.doi.org/10.1007/s11427-018-9455-2DOI Listing
May 2019

Altered serum levels of type I collagen turnover indicators accompanied by IL-6 and IL-8 release in stable COPD.

Int J Chron Obstruct Pulmon Dis 2019;14:163-168. Epub 2019 Jan 3.

Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,

Background: COPD, characterized by chronic inflammation and airway remodeling, has significant pathological alterations in composition and deposition of the extracellular matrix. The expression of procollagen 1 C-terminal peptide (PICP) and collagen type 1 C-terminal telopeptide (ICTP), two major by-products in the synthesis and degradation of collagen, was shown to be positively correlated with inflammatory mediator levels in previous studies.

Purpose: In this study, we investigated whether the serum concentrations of PICP and ICTP were associated with the inflammation level for patients with stable COPD.

Patients And Methods: We collected serum samples from 25 control subjects and 20 patients with stable COPD from December 2011 to October 2012 in Shanghai Zhongshan Hospital and Shanghai Dahua Hospital. We determined concentrations of PICP, ICTP, C-reactive protein (CRP), IL-6, IL-8, and tumor necrosis factor (TNF)-α by using enzyme-linked immunosorbent assay methods.

Results: Demographic characteristics were comparable between the two groups. In patients with stable COPD, serum levels of CRP, IL-6, IL-8, and TNF-α were all elevated compared to control subjects, but only changes of IL-6 achieved statistical significance. Serum concentration of PICP was significantly elevated in patients with COPD, and level of ICTP was slightly decreased. Moreover, serum concentrations of PICP were positively correlated with the levels of both IL-6 and IL-8.

Conclusion: The increased levels of serum PICP in COPD might indicate the condition of airway remodeling, and IL-6 and/or IL-8 might play an important role in stimulating collagen synthesis.
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http://dx.doi.org/10.2147/COPD.S188139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322508PMC
July 2019

Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in .

Evol Appl 2018 Dec 24;11(10):1931-1945. Epub 2018 Sep 24.

Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Tree Breeding College of Biological Sciences and Technology Beijing Forestry University Beijing China.

The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for .
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http://dx.doi.org/10.1111/eva.12697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231471PMC
December 2018

The mortality risk factor of community acquired pneumonia patients with chronic obstructive pulmonary disease: a retrospective cohort study.

BMC Pulm Med 2018 Jan 22;18(1):12. Epub 2018 Jan 22.

Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China.

Background: Chronic obstructive pulmonary disease (COPD) is one of the most common comorbidities in community acquired pneumonia (CAP) patients. We aimed to investigate the characteristics and mortality risk factors of COPD patients hospitalized with CAP.

Methods: A retrospective cohort study was conducted at Shanghai Pulmonary Hospital and Shanghai Dahua Hospital. Clinical and demographic data in patients diagnosed with CAP were collected between January 2015 and June 2016. Logistic regression analysis was performed to screen mortality risk factors of COPD patients hospitalized with CAP.

Results: Of the total 520 CAP patients, 230 (44.2%) patients had been diagnosed comorbid with COPD (COPD-CAP). CAP patients comorbid with COPD patients had higher rate of need for ICU admission (18.3% vs 13.1%) and need for NIMV (26.1% vs 1.4%) than without COPD (nCOPD-CAP). The PSI, CURB-65 and APACHE-II scores in COPD-CAP patients were higher than that in nCOPD-CAP patients (95 vs 79, P < 0.001; 1 vs 1, P < 0.001; 13 vs 8, P < 0.001, respectively). Logistic regression analysis indicated that aspiration, D-dimer > 2.0 μg/mL and CURB-65 ≥ 3 were risk factors associated with in-hospital mortality ((odd ratio) OR = 5.678, OR = 4.268, OR = 20.764, respectively) in COPD-CAP patients. The risk factors associated with 60-day mortality in COPD-CAP patients were comorbid with coronary heart disease, aspiration, need for NIMV (non-invasive mechanical ventilation) and CURB-65 ≥ 3 (OR = 5.206, OR = 7.921, OR = 3.974, OR = 18.002, respectively).

Conclusions: COPD patients hospitalized with CAP had higher rate of need for NIMV, need for ICU admission and severity scores than those without COPD. Aspiration, D-dimer > 2.0 μg/mL, comorbid with coronary heart disease, need for NIMV and CURB-65 ≥ 3 were mortality risk factors in CAP patients comorbid with COPD.
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http://dx.doi.org/10.1186/s12890-018-0587-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778745PMC
January 2018

Evolution and Function of the Populus SABATH Family Reveal That a Single Amino Acid Change Results in a Substrate Switch.

Plant Cell Physiol 2018 Feb;59(2):392-403

College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.

Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyze methylation of the carboxyl group of various low molecular weight metabolites. Investigation of the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Previous studies identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression and biochemical analyses of this large gene family. Twenty-eight Populus SABATH genes were divided into three classes with distinct divergences in their gene structure, expression responses to abiotic stressors and enzymatic properties of encoded proteins. Populus class I SABATH proteins converted IAA to methyl-IAA, class II SABATH proteins converted benzoic acid (BA) and salicylic acid (SA) to methyl-BA and methyl-SA, while class III SABATH proteins converted farnesoic acid (FA) to methyl-FA. For Populus class II SABATH proteins, both forward and reverse mutagenesis studies showed that a single amino acid switch between PtSABATH4 and PtSABATH24 resulted in substrate switch. Our findings provide new insights into the evolution of substrate specificities of enzyme families.
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http://dx.doi.org/10.1093/pcp/pcx198DOI Listing
February 2018

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).

Mol Biol Evol 2017 07;34(7):1689-1701

Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden.

Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ∼35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.
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http://dx.doi.org/10.1093/molbev/msx111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455968PMC
July 2017

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae).

Sci Rep 2016 10 10;6:34821. Epub 2016 Oct 10.

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average H = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.
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http://dx.doi.org/10.1038/srep34821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056456PMC
October 2016

Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change.

Sci Rep 2016 05 23;6:26613. Epub 2016 May 23.

Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China.

Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
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http://dx.doi.org/10.1038/srep26613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876407PMC
May 2016

De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.

PLoS One 2016 16;11(2):e0148985. Epub 2016 Feb 16.

National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148985PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755536PMC
July 2016

Molecular Properties and Functional Divergence of the Dehydroascorbate Reductase Gene Family in Lower and Higher Plants.

PLoS One 2015 18;10(12):e0145038. Epub 2015 Dec 18.

National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

Dehydroascorbate reductase (DHAR), which reduces oxidized ascorbate, is important for maintaining an appropriate ascorbate redox state in plant cells. To date, genome-wide molecular characterization of DHARs has only been conducted in bryophytes (Physcomitrella patens) and eudicots (e.g. Arabidopsis thaliana). In this study, to gain a general understanding of the molecular properties and functional divergence of the DHARs in land plants, we further conducted a comprehensive analysis of DHARs from the lycophyte Selaginella moellendorffii, gymnosperm Picea abies and monocot Zea mays. DHARs were present as a small gene family in all of the land plants we examined, with gene numbers ranging from two to four. All the plants contained cytosolic and chloroplastic DHARs, indicating dehydroascorbate (DHA) can be directly reduced in the cytoplasm and chloroplast by DHARs in all the plants. A novel vacuolar DHAR was found in Z. mays, indicating DHA may also be reduced in the vacuole by DHARs in Z. mays. The DHARs within each species showed extensive functional divergence in their gene structures, subcellular localizations, and enzymatic characteristics. This study provides new insights into the molecular characteristics and functional divergence of DHARs in land plants.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145038PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687524PMC
July 2016

Predicting Impacts of Future Climate Change on the Distribution of the Widespread Conifer Platycladus orientalis.

PLoS One 2015 1;10(7):e0132326. Epub 2015 Jul 1.

National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species' distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2×106 km2 across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132326PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488561PMC
May 2016

Association of SLCO1B1 gene polymorphisms with toxicity response of high dose methotrexate chemotherapy in childhood acute lymphoblastic leukemia.

Int J Clin Exp Med 2015 15;8(4):6109-13. Epub 2015 Apr 15.

Department of Hematology and Oncology, Children's Hospital of Fudan University No. 399 Wanyuan Road, Shanghai, 201102, P.R. China.

Objective: The present study aims to investigate the correlation of polymorphisms of SLCO1B1 gene with the toxicity during therapy with the high-dose methotrexate (MTX) chemotherapy in childhood acute lymphoblastic leukemia.

Methods: We analyzed 2 polymorphisms (rs4149081 and rs11045897) in SLCO1B1 gene in 280 Chinese pediatric B-ALL patients, using MTX plasma concentration as an objective and quantifiable marker of toxicity. We utilized Enzyme-multiplied immunoassay technique (EMIT) to measure the plasma concentration of MTX. The polymerase chain reaction-allele specific (PCR-AS) method was utilized to perform the genotyping.

Results: We found there was a statistically significant association between MTX plasma concentration and the SLCO1B1 rs11045879 CC genotype (P<0.05). We also found the rs4149081 AA genotype was associated with high-MTX plasma concentrations. A-C haplotype carriers have a higher risk for MTX delayed clearance but G-T haplotype was associated with a lower risk for MTX delayed clearance.

Conclusions: The rs4149081 AA genotype and the rs11045897 CC genotype could be indicators for high-MTX plasma concentrations in children with ALL.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4483916PMC
July 2015

[Study on fluorescence labeling and determination of polypeptide (PC2~PC6) by high performance liquid chromatography].

Guang Pu Xue Yu Guang Pu Fen Xi 2014 Dec;34(12):3301-6

This study was based on the thiol groups (-SH) of PC2~PC6, which could be reacted with the Monobromobimane (mBBr), in order to get polypeptide derivatives with fluorescent signal. A new method was developed for measuring the Polypeptides by high performance liquid chromatography with fluorescence detector, then the chromatographic conditions of HPLC was optimized; meawhile the reaction proportion of PCs and mBBr was identified by Trap-MS. The results showed that, the reaction proportion of PCs and mBBr was 1:1, the polypeptide derivatives had good stability; the five compounds separation was better, and the peak time focused on the 16.6~22.0 min; the linear correlation coefficient of PC2, PC3, PC4, PC5 and PC6 was >0.9991, and the limits of quantification were 0.3, 0.05, 0.3, 0.5 and 0.8 mg · L(-1) respectively, the recovery rate was 83.0%-102.0%; the method was reproducible, RSD<2%, this method for measuring the peptide compounds was rapid and accurate.
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December 2014

Adaptive differentiation in seedling traits in a hybrid pine species complex, Pinus densata and its parental species, on the Tibetan Plateau.

PLoS One 2015 10;10(3):e0118501. Epub 2015 Mar 10.

State Engineering Laboratory of Forest Tree Breeding, Key Laboratory of Genetic and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing, China; College of Biology Sciences and Technology, Beijing Forestry University, Beijing, China.

Evidence from molecular genetics demonstrates that Pinus densata is a natural homoploid hybrid originating from the parent species Pinus tabuliformis and Pinus yunnanensis, and ecological selection may have played a role in the speciation of P. densata. However, data on differentiation in adaptive traits in the species complex are scarce. In this study, we performed a common garden test on 16 seedling traits to examine the differences between P. densata and its parental species in a high altitude environment. We found that among the 16 analyzed traits, 15 were significantly different among the species. Pinus tabuliformis had much earlier bud set and a relatively higher bud set ratio but poorer seedling growth, and P. yunnanensis had opposite responses for the same traits. P. densata had the greatest fitness with higher viability and growth rates than the parents. The relatively high genetic contribution of seedling traits among populations suggested that within each species the evolutionary background is complex. The correlations between the seedling traits of a population within a species and the environmental factors indicated different impacts of the environment on species evolution. The winter temperature is among the most important climate factors that affected the fitness of the three pine species. Our investigation provides empirical evidence on adaptive differentiation among this pine species complex at seedling stages.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118501PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355066PMC
January 2016

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers.

Mol Ecol Resour 2015 Jul 20;15(4):711-22. Epub 2014 Nov 20.

Department of Ecology and Environmental Science, Umeå University, Umeå, SE-90187, Sweden.

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.
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http://dx.doi.org/10.1111/1755-0998.12342DOI Listing
July 2015
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