Genome sequence of cultivated Upland cotton ( Gossypium hirsutum TM-1) provides insights into genome evolution
Fuguang Li,Guangyi Fan,Cairui Lu,Guanghui Xiao,Changsong Zou,Russell J. Kohel,Zhiying Ma,Haihong Shang,Xiongfeng Ma,Jianyong Wu,Xinming Liang,Gai Huang,Richard G. Percy,Kun Liu,Weihua Yang,Wenbin Chen,Xiongming Du,Chengcheng Shi,Youlu Yuan,Wuwei Ye,Xin Liu,Xueyan Zhang,Weiqing Liu,Hengling Wei,Shoujun Wei,Guodong Huang,Xianlong Zhang,Shuijin Zhu,He Zhang,Fengming Sun,Xingfen Wang,Jie Liang,Jiahao Wang,Qiang He,Leihuan Huang,Jun Wang,Jinjie Cui,Guoli Song,Kunbo Wang,Xun Xu,John Z. Yu,Yu-Xian Zhu,Shuxun Yu +42 more
TLDR
A draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map is produced for G. hirsutum, revealing conserved gene order and concerted evolution of different regulatory mechanisms for Cellulose synthase and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 may be important for enhanced fiber production.Abstract:
Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.read more
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Journal ArticleDOI
Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Tianzhen Zhang,Yan Hu,Wenkai Jiang,Lei Fang,Xueying Guan,Jiedan Chen,Jinbo Zhang,Christopher A. Saski,Brian E. Scheffler,David M. Stelly,Amanda M. Hulse-Kemp,Qun Wan,Bingliang Liu,Chunxiao Liu,Sen Wang,Mengqiao Pan,Yangkun Wang,Dawei Wang,Wenxue Ye,Lijing Chang,Wenpan Zhang,Qingxin Song,Ryan C. Kirkbride,Xiao-Ya Chen,Elizabeth S. Dennis,Danny J. Llewellyn,Daniel G. Peterson,Peggy Thaxton,Don C. Jones,Qiong Wang,Xiaoyang Xu,Hua Zhang,Huaitong Wu,Lei Zhou,Gaofu Mei,Shuqi Chen,Yue Tian,Dan Xiang,Xinghe Li,Jian Ding,Qiyang Zuo,Linna Tao,Yunchao Liu,Ji Li,Yu Lin,Yuanyuan Hui,Zhisheng Cao,Caiping Cai,Xiefei Zhu,Zhi Jiang,Baoliang Zhou,Wangzhen Guo,Ruiqiang Li,Z. Jeffrey Chen +53 more
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.
Journal ArticleDOI
Evolution of Gene Duplication in Plants.
TL;DR: This review surveys the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.
Journal ArticleDOI
The genome of Chenopodium quinoa
David Erwin Jarvis,Yung Shwen Ho,Damien J. Lightfoot,Sandra M. Schmöckel,Bo Li,Theo Borm,Hajime Ohyanagi,Katsuhiko Mineta,Craig T. Michell,Noha Saber,Najeh M. Kharbatia,Ryan R. Rupper,Aaron R. Sharp,Nadine Dally,Berin A. Boughton,Yong H. Woo,Ge Gao,Elio Schijlen,Xiujie Guo,Afaque Ahmad Imtiyaz Momin,Sónia Negrão,Salim Al-Babili,Christoph A Gehring,Ute Roessner,Christian Jung,Kevin Murphy,Stefan T. Arold,Takashi Gojobori,C. Gerard van der Linden,Eibertus N. van Loo,Eric N. Jellen,Peter J. Maughan,Mark Tester +32 more
TL;DR: The assembly of a high-quality, chromosome-scale reference genome sequence for quinoa was produced using single-molecule real-time sequencing in combination with optical, chromosomes-contact and genetic maps, which facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds.
Journal ArticleDOI
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.
Yan Hu,Yan Hu,Jiedan Chen,Lei Fang,Lei Fang,Zhiyuan Zhang,Wei Ma,Yongchao Niu,Longzhen Ju,Jieqiong Deng,Ting Zhao,Ting Zhao,Jinmin Lian,Kobi Baruch,David D. Fang,Xia Liu,Yong-Ling Ruan,Yong-Ling Ruan,Mehboob-ur Rahman,Jinlei Han,Kai Wang,Qiong Wang,Huaitong Wu,Gaofu Mei,Yihao Zang,Zegang Han,Chenyu Xu,Weijuan Shen,Duofeng Yang,Zhanfeng Si,Fan Dai,Liangfeng Zou,Fei Huang,Bai Yulin,Yu-Gao Zhang,Avital Brodt,Hilla Ben-Hamo,Xiefei Zhu,Baoliang Zhou,Xueying Guan,Xueying Guan,Shuijin Zhu,Xiao-Ya Chen,Tianzhen Zhang,Tianzhen Zhang +44 more
TL;DR: High-quality de novo–assembled genomes of two cultivated allotetraploid cotton species and whole-genome comparative analyses provide insights into the evolution of cotton genomes and improvement of fiber quality and resilience to stress.
Journal ArticleDOI
CRISPR for Crop Improvement: An Update Review.
Deepa Jaganathan,Karthikeyan Ramasamy,Gothandapani Sellamuthu,Shilpha Jayabalan,Gayatri Venkataraman +4 more
TL;DR: Application of CRISPR/Cas9 techniques will result in the development of non-genetically modified (Non-GMO) crops with the desired trait that can contribute to increased yield potential under biotic and abiotic stress conditions.
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