scispace - formally typeset
Search or ask a question
Author

Shunmou Huang

Bio: Shunmou Huang is an academic researcher from Crops Research Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 22, co-authored 24 publications receiving 3713 citations. Previous affiliations of Shunmou Huang include Huazhong Agricultural University.
Topics: Genome, Gene, Biology, Transcriptome, SNP genotyping

Papers
More filters
Journal ArticleDOI
Xiaowu Wang1, Hanzhong Wang, Jun Wang2, Jun Wang3, Jun Wang4, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai3, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang3, Xiyin Wang7, Xiyin Wang8, Michael Freeling9, J. Chris Pires10, Andrew H. Paterson7, Boulos Chalhoub, Bo Wang3, Alice Hayward11, Alice Hayward12, Andrew G. Sharpe13, Beom-Seok Park5, Bernd Weisshaar14, Binghang Liu3, Bo Li3, Bo Liu, Chaobo Tong, Chi Song3, Chris Duran15, Chris Duran12, Chunfang Peng3, Geng Chunyu3, Chushin Koh13, Chuyu Lin3, David Edwards12, David Edwards15, Desheng Mu3, Di Shen, Eleni Soumpourou6, Fei Li, Fiona Fraser6, Gavin C. Conant10, Gilles Lassalle16, Graham J.W. King4, Guusje Bonnema17, Haibao Tang9, Haiping Wang, Harry Belcram, Heling Zhou3, Hideki Hirakawa, Hiroshi Abe, Hui Guo7, Hui Wang, Huizhe Jin7, Isobel A. P. Parkin18, Jacqueline Batley11, Jacqueline Batley12, Jeong-Sun Kim5, Jérémy Just, Jianwen Li3, Jiaohui Xu3, Jie Deng, Jin A Kim5, Jingping Li7, Jingyin Yu, Jinling Meng19, Jinpeng Wang8, Jiumeng Min3, Julie Poulain20, Katsunori Hatakeyama, Kui Wu3, Li Wang8, Lu Fang, Martin Trick6, Matthew G. Links18, Meixia Zhao, Mina Jin5, Nirala Ramchiary21, Nizar Drou22, Paul J. Berkman15, Paul J. Berkman12, Qingle Cai3, Quanfei Huang3, Ruiqiang Li3, Satoshi Tabata, Shifeng Cheng3, Shu Zhang3, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon5, Su-Ryun Choi21, Tae-Ho Lee7, Wei Fan3, Xiang Zhao3, Xu Tan7, Xun Xu3, Yan Wang, Yang Qiu, Ye Yin3, Yingrui Li3, Yongchen Du, Yongcui Liao, Yong Pyo Lim21, Yoshihiro Narusaka, Yupeng Wang8, Zhenyi Wang8, Zhenyu Li3, Zhiwen Wang3, Zhiyong Xiong10, Zhonghua Zhang 
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

1,811 citations

Journal ArticleDOI
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Abstract: Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus

884 citations

Journal ArticleDOI
TL;DR: The sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame, an important species from the order Lamiales and a high oil crop.
Abstract: Background: Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored. Results: Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame. Conclusions: As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.

225 citations

Journal ArticleDOI
TL;DR: The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.
Abstract: Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3’end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge. In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3’ end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species. The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low- to moderate- throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.

205 citations

Journal ArticleDOI
TL;DR: The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11', and certain genetic differences were also detected in two morphotypes.
Abstract: Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.

186 citations


Cited by
More filters
Journal ArticleDOI
Boulos Chalhoub1, Shengyi Liu2, Isobel A. P. Parkin3, Haibao Tang4, Haibao Tang5, Xiyin Wang6, Julien Chiquet1, Harry Belcram1, Chaobo Tong2, Birgit Samans7, Margot Correa8, Corinne Da Silva8, Jérémy Just1, Cyril Falentin9, Chu Shin Koh10, Isabelle Le Clainche1, Maria Bernard8, Pascal Bento8, Benjamin Noel8, Karine Labadie8, Adriana Alberti8, Mathieu Charles9, Dominique Arnaud1, Hui Guo6, Christian Daviaud, Salman Alamery11, Kamel Jabbari12, Kamel Jabbari1, Meixia Zhao13, Patrick P. Edger14, Houda Chelaifa1, David C. Tack15, Gilles Lassalle9, Imen Mestiri1, Nicolas Schnel9, Marie-Christine Le Paslier9, Guangyi Fan, Victor Renault16, Philippe E. Bayer11, Agnieszka A. Golicz11, Sahana Manoli11, Tae-Ho Lee6, Vinh Ha Dinh Thi1, Smahane Chalabi1, Qiong Hu2, Chuchuan Fan17, Reece Tollenaere11, Yunhai Lu1, Christophe Battail8, Jinxiong Shen17, Christine Sidebottom10, Xinfa Wang2, Aurélie Canaguier1, Aurélie Chauveau9, Aurélie Bérard9, G. Deniot9, Mei Guan18, Zhongsong Liu18, Fengming Sun, Yong Pyo Lim19, Eric Lyons20, Christopher D. Town5, Ian Bancroft21, Xiaowu Wang, Jinling Meng17, Jianxin Ma13, J. Chris Pires22, Graham J.W. King23, Dominique Brunel9, Régine Delourme9, Michel Renard9, Jean-Marc Aury8, Keith L. Adams15, Jacqueline Batley11, Jacqueline Batley24, Rod J. Snowdon7, Jörg Tost, David Edwards11, David Edwards24, Yongming Zhou17, Wei Hua2, Andrew G. Sharpe10, Andrew H. Paterson6, Chunyun Guan18, Patrick Wincker25, Patrick Wincker1, Patrick Wincker8 
22 Aug 2014-Science
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

1,743 citations

Journal ArticleDOI
TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

1,221 citations

Journal ArticleDOI
20 Dec 2012-Nature
TL;DR: It is shown that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago, conferred about 30–36-fold duplication of ancestral angiosperm genes in elite cottons, genetic complexity equalled only by Brassica among sequenced angiosperms.
Abstract: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

1,015 citations

Journal ArticleDOI
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Abstract: Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus

884 citations