Publications by authors named "Ray Ming"

152 Publications

Rambutan genome revealed gene networks for spine formation and aril development.

Plant J 2021 Sep 13. Epub 2021 Sep 13.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 6180, USA.

Rambutan is a popular tropical fruit known for its exotic appearance, has long flexible spines on shells, extraordinary aril growth, desirable nutrition, and a favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed that rambutan chromosomes 8 and 12 are collinear with lychee chromosome 1, which resulted in a chromosome fission event in rambutan (n = 16) or a fusion event in lychee (n = 15) after their divergence from a common ancestor 15.7 million years ago. Root development genes played a crucial role in spine development, such as endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and K transport genes. Aril development was regulated by D-class genes (STK and SHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar metabolism genes. The lower rate of male sterility of hermaphroditic flowers appears to be regulated by MYB24. Population genomic analyses revealed genes in selective sweeps during domestication that are related to fruit morphology and environment stress response. These findings enhance our understanding of spine and aril development and provide genomic resources for rambutan improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15491DOI Listing
September 2021

Identification of structural variation and polymorphisms of a sex co-segregating scaffold in spinach.

Plant Reprod 2021 Jul 28. Epub 2021 Jul 28.

Department of Plant Biology, University of Illinois At Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL, 61801-3838, USA.

Spinach is a common vegetable, and dioecy is maintained by a pair of XY sex chromosomes. Due to limited genomic resources and its highly repetitive genome, limited studies were conducted to investigate the genomic landscape of the region near sex-determining loci. In this study, we screened the structure variations (SVs) between Y-linked contigs and a 1.78-Mb X scaffold (Super_scaffold 66), which enabled the development of 12 sex co-segregating DNA markers. These markers were tested in one F mapping population and 40 spinach accessions, which comprised 692 individual plants with the strong sex linkage pattern. In addition, we found that Super_scaffold 66 was highly repetitive along with the enriched LTR-RTs insertions and decreased microsatellite distribution compared with the rest genome, which matches extremely low gene density featured by only nine annotated genes. Synteny analysis between Y contigs and Superscaffold_66 revealed a 340-Kb accumulative Y contig (non-continuous) and a 500-Kb X counterpart along with SVs and wide-spread tandem duplications. Among the nine genes, one ABC transporter gene revealed noticeable SVs between Y contig and X counterpart, as an approximate 5-Kb recent Gypsy LTR-RT insertion in the Y-linked allele, but not the X allele. The gene paucity, SVs, and sex-linked polymorphisms attributed to the recombination suppression. We proposed that Super_scaffold 66 is part of the non-recombining region containing the sex determination genes. The spread of 12 sex co-segregating markers from this 1.78 Mb genomic region indicated the existence and expansion of sex determination region during progression of the Y chromosome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00497-021-00424-1DOI Listing
July 2021

Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis.

Nat Genet 2021 08 15;53(8):1250-1259. Epub 2021 Jul 15.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Tea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-021-00895-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346365PMC
August 2021

Expression profiling of the Dof gene family under abiotic stresses in spinach.

Sci Rep 2021 07 13;11(1):14429. Epub 2021 Jul 13.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

DNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-93383-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8277872PMC
July 2021

Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers.

Hortic Res 2021 Jul 1;8(1):147. Epub 2021 Jul 1.

FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.

Sex types of papaya are controlled by a pair of nascent sex chromosomes, but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still unclear. We performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers. A total of 1734 differentially expressed genes (DEGs) were identified, of which 923 showed female-biased expression and 811 showed male-biased expression. Functional annotation revealed that genes related to plant hormone biosynthesis and signaling pathways, especially in abscisic acid and auxin pathways, were overrepresented in the DEGs. Transcription factor binding motifs, such as MYB2, GAMYB, and AP2/EREBP, were enriched in the promoters of the hormone-related DEGs, and transcription factors with those motifs also exhibited differential expression between sex types. Among these DEGs, we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel development. Our results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional, epigenetic, and phytohormone regulation. Hormones, especially ABA and auxin, transcription factors, and genes in the non-recombination region of the sex chromosome could be involved in this process. Our findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41438-021-00581-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245580PMC
July 2021

Reference genomes of the two cultivated jute species.

Plant Biotechnol J 2021 Jun 25. Epub 2021 Jun 25.

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.

Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.13652DOI Listing
June 2021

Somatic variations led to the selection of acidic and acidless orange cultivars.

Nat Plants 2021 07 17;7(7):954-965. Epub 2021 Jun 17.

Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, P. R. China.

Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-021-00941-xDOI Listing
July 2021

Editorial: Genomics-Enabled Crop Genetics.

Front Genet 2021 7;12:687160. Epub 2021 May 7.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2021.687160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138204PMC
May 2021

Unraveling a genetic roadmap for improved taste in the domesticated apple.

Mol Plant 2021 Sep 19;14(9):1454-1471. Epub 2021 May 19.

Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. Electronic address:

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molp.2021.05.018DOI Listing
September 2021

Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association.

Nat Ecol Evol 2021 07 17;5(7):974-986. Epub 2021 May 17.

Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.

Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41559-021-01469-1DOI Listing
July 2021

Structural variations in papaya genomes.

BMC Genomics 2021 May 10;22(1):335. Epub 2021 May 10.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Background: Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers.

Results: We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress.

Conclusions: SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-021-07665-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8108470PMC
May 2021

The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae.

Nat Plants 2021 05 6;7(5):608-618. Epub 2021 May 6.

State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China.

Miscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus. Fusion of two chromosomes occurred during rediploidization in M. floridulus and no significant subgenome dominance was observed. A survey of cellulose synthases (CesA) in M. floridulus revealed quite high expression of most CesA genes in growing stems, which is in agreement with the high cellulose content of this species. Resequencing and comparisons of 75 Miscanthus accessions suggest that M. lutarioriparius is genetically close to M. sacchariflorus and that M. floridulus is more distantly related to other species and is more genetically diverse. This study provides a valuable genomic resource for molecular breeding and improvement of Miscanthus and Saccharinae crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-021-00908-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238680PMC
May 2021

Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach.

BMC Plant Biol 2021 Apr 6;21(1):166. Epub 2021 Apr 6.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Background: Pollination accelerate sepal development that enhances plant fitness by protecting seeds in female spinach. This response requires pollination signals that result in the remodeling within the sepal cells for retention and development, but the regulatory mechanism for this response is still unclear. To investigate the early pollination-induced metabolic changes in sepal, we utilize the high-throughput RNA-seq approach.

Results: Spinach variety 'Cornel 9' was used for differentially expressed gene analysis followed by experiments of auxin analog and auxin inhibitor treatments. We first compared the candidate transcripts expressed differentially at different time points (12H, 48H, and 96H) after pollination and detected significant difference in Trp-dependent auxin biosynthesis and auxin modulation and transduction process. Furthermore, several auxin regulatory pathways i.e. cell division, cell wall expansion, and biogenesis were activated from pollination to early developmental symptoms in sepals following pollination. To further confirm the role auxin genes play in the sepal development, auxin analog (2, 4-D; IAA) and auxin transport inhibitor (NPA) with different concentrations gradient were sprayed to the spinach unpollinated and pollinated flowers, respectively. NPA treatment resulted in auxin transport weakening that led to inhibition of sepal development at concentration 0.1 and 1 mM after pollination. 2, 4-D and IAA treatment to unpollinated flowers resulted in sepal development at lower concentration but wilting at higher concentration.

Conclusion: We hypothesized that sepal retention and development might have associated with auxin homeostasis that regulates the sepal size by modulating associated pathways. These findings advanced the understanding of this unusual phenomenon of sepal growth instead of abscission after pollination in spinach.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12870-021-02944-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022616PMC
April 2021

Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus.

J Genet Genomics 2021 01 15;48(1):75-87. Epub 2021 Feb 15.

Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address:

Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events in Aragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgg.2021.01.002DOI Listing
January 2021

Transcriptional regulation of dosage compensation in Carica papaya.

Sci Rep 2021 Mar 12;11(1):5854. Epub 2021 Mar 12.

Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, USA.

Sex chromosome evolution results in the disparity in gene content between heterogametic sex chromosomes and creates the need for dosage compensation to counteract the effects of gene dose imbalance of sex chromosomes in males and females. It is not known at which stage of sex chromosome evolution dosage compensation would evolve. We used global gene expression profiling in male and female papayas to assess gene expression patterns of sex-linked genes on the papaya sex chromosomes. By analyzing expression ratios of sex-linked genes to autosomal genes and sex-linked genes in males relative to females, our results showed that dosage compensation was regulated on a gene-by-gene level rather than whole sex-linked region in papaya. Seven genes on the papaya X chromosome exhibited dosage compensation. We further compared gene expression ratios in the two evolutionary strata. Y alleles in the older evolutionary stratum showed reduced expression compared to X alleles, while Y alleles in the younger evolutionary stratum showed elevated expression compared to X alleles. Reduced expression of Y alleles in the older evolutionary stratum might be caused by accumulation of deleterious mutations in regulatory regions or transposable element-mediated methylation spreading. Most X-hemizygous genes exhibited either no or very low expression, suggesting that gene silencing might play a role in maintaining transcriptional balance between females and males.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-85480-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971000PMC
March 2021

Ultra-long DNA molecule isolation from plant nuclei for ultra-long read genome sequencing.

STAR Protoc 2021 Mar 17;2(1):100343. Epub 2021 Feb 17.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Long and ultra-long read DNA sequencing technologies require high molecular weight DNA with high quality and sufficient quantity, which could be challenging to obtain from recalcitrant plant tissues. We describe a protocol to isolate ultra-long DNA from 12 species for ultra-long read genome sequencing. A suitable nuclei lysis buffer is critical for DNA quality and yield. This protocol will enable individual labs to isolate high molecular weight DNA at a rapid pace with low cost from a variety of plant species. For complete information on the use and execution of this protocol, please refer to: Zhang et al. (2020).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xpro.2021.100343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902544PMC
March 2021

The complete chloroplast genome sequence of cultivar Tieguanyin (Theaceae).

Mitochondrial DNA B Resour 2021 Feb 8;6(2):395-396. Epub 2021 Feb 8.

College of Life Science, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.

cultivar Tieguanyin (TGY) is an important Oolong tea variety in China. In this study, we reported a complete chloroplast (cp) genome based on the Illumina sequencing technology and combined and reference-guided assembly strategies. The complete cp genome of 'TGY' displayed the regular quadripartite structure: a total of 157,126 bp in length, comprising a large single-copy (LSC, 86,904 bp) region, a small single-copy (SSC, 18,532 bp) region, and a pair of inverted repeats (IRs, 26,095 bp) regions. A lot of 132 predicted genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content is 37.3%. Maximum likelihood (ML) phylogenetic tree involving 18 cp genomes of the genus revealed a relatively independent event of local domestication among three types of cultivars. The complete cp genome of 'TGY' provides an insight into tea plants for further understanding evolutionary research on tea plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2020.1869615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7872547PMC
February 2021

Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae.

Plants (Basel) 2021 Feb 2;10(2). Epub 2021 Feb 2.

Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Rambutan ( L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that , , , , and were under positive selection, which might reflect specific adaptations of to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that chloroplast genome has the closest relationship with that of . The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants10020283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912957PMC
February 2021

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism.

Nat Commun 2021 02 2;12(1):718. Epub 2021 Feb 2.

CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-20957-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854680PMC
February 2021

The complete chloroplast genome of a gynodioecious deciduous orchid (Orchidaceae) female.

Mitochondrial DNA B Resour 2019 Nov 8;4(2):3876-3877. Epub 2019 Nov 8.

FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, The Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization (Fuzhou), College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.

The chloroplast (cp) genome sequence of a gynodioecious female type has been characterized using Illumina pair-end sequencing. The complete cp genome was 154,418 bp in length, containing a large single copy region (LSC) of 83,475 bp and a small single copy region (SSC) of 17,513 bp, which were separated by a pair of 26,715 bp inverted repeat regions (IRs). The genome contained 132 genes, with 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.18% with the values of the LSC, SSC, and IR regions are 34.90%, 30.15%, and 43.06%, respectively. Phylogenetic analysis suggested that the is close to (MG925368) in subfamily Orchidoideae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/23802359.2019.1687359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707742PMC
November 2019

The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine.

Plant J 2021 03 21;105(6):1495-1506. Epub 2021 Jan 21.

Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China.

Vitis amurensis (Shanputao) is the most cold tolerant Vitis species and so is of great interest to grape breeders and producers in areas with low winter temperatures. Here, we report its high-quality, chromosome-level genome assembly based on a combination of sequence data from Illumina and PacBio platforms, BioNano optical mapping and high-throughput chromosome conformation Capture (Hi-C) mapping. The 604.56-Mb genome contains 32 885 protein-coding genes. Shanputao was found to share a common ancestor with PN40024 (V. vinifera) approximately 2.17-2.91 million years ago, and gene expansion observed in Shanputao might contribute to the enhancement of cold tolerance. Transcriptome analysis revealed 17 genes involved in cold signal transduction, suggesting that there was a different response mechanism to chilling temperature and freezing conditions. Furthermore, a genome-wide association study uncovered a phosphoglycerate kinase gene that may contribute to the freezing resistance of buds in the winter. The Shanputao genome sequence not only represents a valuable resource for grape breeders, but also is important for clarifying the molecular mechanisms involved in cold tolerance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15127DOI Listing
March 2021

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum.

Sci Rep 2020 11 25;10(1):20536. Epub 2020 Nov 25.

College of Agriculture, FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-77375-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688973PMC
November 2020

Evolutionary expansion and functional divergence of sugar transporters in Saccharum (S. spontaneum and S. officinarum).

Plant J 2021 02 8;105(4):884-906. Epub 2020 Dec 8.

Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

The sugar transporter (ST) family is considered to be the most important gene family for sugar accumulation, but limited information about the ST family in the important sugar-yielding crop Saccharum is available due to its complex genetic background. Here, 105 ST genes were identified and clustered into eight subfamilies in Saccharum spontaneum. Comparative genomics revealed that tandem duplication events contributed to ST gene expansions of two subfamilies, PLT and STP, in S. spontaneum, indicating an early evolutionary step towards high sugar content in Saccharum. The analyses of expression patterns were based on four large datasets with a total of 226 RNA sequencing samples from S. spontaneum and Saccharum officinarum. The results clearly demonstrated 50 ST genes had different spatiotemporal expression patterns in leaf tissues, 10 STs were specifically expressed in the stem, and 10 STs responded to the diurnal rhythm. Heterologous expression experiments in the defective yeast strain EBY.VW4000 indicated STP13, pGlcT2, VGT3, and TMT4 are the STs with most affinity for glucose/fructose and SUT1_T1 has the highest affinity to sucrose. Furthermore, metabolomics analysis suggested STP7 is a sugar starvation-induced gene and STP13 has a function in retrieving sugar in senescent tissues. PLT11, PLT11_T1, TMT3, and TMT4 contributed to breaking the limitations of the storage sink. SUT1, SUT1_T1, PLT11, TMT4, pGlcT2, and VGT3 responded for different functions in these two Saccharum species. This study demonstrated the evolutionary expansion and functional divergence of the ST gene family and will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15076DOI Listing
February 2021

The evolutionary origin and domestication history of goldfish ().

Proc Natl Acad Sci U S A 2020 11 2;117(47):29775-29785. Epub 2020 Nov 2.

Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2005545117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703540PMC
November 2020

Identification of Candidate Auxin Response Factors Involved in Pomegranate Seed Coat Development.

Front Plant Sci 2020 15;11:536530. Epub 2020 Sep 15.

Key Laboratory of Horticultural Crop Genetic Improvement and Eco-physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China.

Auxin response factors (ARFs) are transcription factors, regulating the auxin signaling pathways involved in plant development and related processes. In this study, we performed the genome-wide identification and characterization of s in pomegranate and compared them with s from three other species. Seventeen PgrARFs were identified and clustered into four groups, according to their phylogenetic relationship with the remaining 59 ARFs. A recent whole-genome duplication event in pomegranate may have contributed to the expansion and diversification of s. Genomic truncation and variant splicing mechanisms contributed to the divergence of s, a conclusion that was supported by different exon-intron structures of genes and incomplete conserved domains of PgrARFs in a specific phylogenetic group (group III). Interestingly, the absence of motifs from certain genes corresponded to their low transcription levels, which contrasted to the highly expressed s with intact motifs. Specifically, and highly expressed in both inner and outer seed coat, and phylogenetically related to orthologs which mediates cell divisions in seed coat. We infer these two might involve in seed coat development through cell divisions in response to auxin regulation. These findings provided information on the characteristics and evolutionary relationships of s, but also shed lights on their potential roles during seed coat development in pomegranate.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.536530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522551PMC
September 2020

Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution.

Cell 2020 11 8;183(4):875-889.e17. Epub 2020 Oct 8.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address:

Banyan trees are distinguished by their extraordinary aerial roots. The Ficus genus includes species that have evolved a species-specific mutualism system with wasp pollinators. We sequenced genomes of the Chinese banyan tree, F. microcarpa, and a species lacking aerial roots, F. hispida, and one wasp genome coevolving with F. microcarpa, Eupristina verticillata. Comparative analysis of the two Ficus genomes revealed dynamic karyotype variation associated with adaptive evolution. Copy number expansion of auxin-related genes from duplications and elevated auxin production are associated with aerial root development in F. microcarpa. A male-specific AGAMOUS paralog, FhAG2, was identified as a candidate gene for sex determination in F. hispida. Population genomic analyses of Ficus species revealed genomic signatures of morphological and physiological coadaptation with their pollinators involving terpenoid- and benzenoid-derived compounds. These three genomes offer insights into and genomic resources for investigating the geneses of aerial roots, monoecy and dioecy, and codiversification in a symbiotic system.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2020.09.043DOI Listing
November 2020

The genomic architecture of the sex-determining region and sex-related metabolic variation in Ginkgobiloba.

Plant J 2020 12 27;104(5):1399-1409. Epub 2020 Oct 27.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex-determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex-determining region of Ginkgo contains more than 200 genes, including four MADS-box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.15009DOI Listing
December 2020
-->