RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants
Pingchuan Li,Xiande Quan,Gaofeng Jia,Gaofeng Jia,Jin Xiao,Jin Xiao,Sylvie Cloutier,Frank M. You +7 more
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TLDR
RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs and was successfully applied to predict RGAs for 50 sequenced plant genomes.Abstract:
Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury
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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
Ming-Cheng Luo,Yong Q. Gu,Daniela Puiu,Hao Wang,Sven Twardziok,Karin R. Deal,Naxin Huo,Naxin Huo,Tingting Zhu,Le Wang,Yi Wang,Yi Wang,Patrick E. McGuire,Shuyang Liu,Hai Long,Ramesh K Ramasamy,Juan C Rodriguez,Sonny Lee Van,Luxia Yuan,Zhenzhong Wang,Zhenzhong Wang,Zhiqiang Xia,Lichan Xiao,Olin D. Anderson,Shuhong Ouyang,Shuhong Ouyang,Yong Liang,Yong Liang,Aleksey V. Zimin,Geo Pertea,Peng Qi,Jeffrey L. Bennetzen,Xiongtao Dai,Matthew W Dawson,Hans-Georg Müller,Karl G. Kugler,Lorena Rivarola-Duarte,Manuel Spannagl,Klaus F. X. Mayer,Fu-Hao Lu,Michael W. Bevan,Philippe Leroy,Pingchuan Li,Frank M. You,Qixin Sun,Zhiyong Liu,Eric Lyons,Thomas Wicker,Steven L. Salzberg,Steven L. Salzberg,Katrien M. Devos,Jan Dvořák +51 more
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Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat
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TL;DR: It is demonstrated that Fhb7, when introgressed into diverse wheat backgrounds by distant hybridization, confers broad resistance to both FHB and crown rot without penalizing wheat yield and is suggested a source of Fusarium resistance for wheat improvement.
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A route to de novo domestication of wild allotetraploid rice
Hong Yu,Tao Lin,Xiangbing Meng,Huilong Du,Jingkun Zhang,Guifu Liu,Mingjiang Chen,Yanhui Jing,Liquan Kou,Xiuxiu Li,Qiang Gao,Yan Liang,Xiangdong Liu,Zhilan Fan,Yuntao Liang,Zhukuan Cheng,Mingsheng Chen,Zhixi Tian,Yonghong Wang,Chengcai Chu,Jianru Zuo,Jianmin Wan,Qian Qian,Bin Han,Andrea Zuccolo,Andrea Zuccolo,Rod A. Wing,Rod A. Wing,Caixia Gao,Chengzhi Liang,Jiayang Li +30 more
TL;DR: Zhang et al. as discussed by the authors proposed a de novo domestication of wild allotetraploid rice by screening a wild rice inventory, and identified one genotype of Oryza alta (CCDD), polyploid Rice 1 (PPR1), and established two important resources for its de-no-vovo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece.
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Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics
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Construction and comparison of three reference-quality genome assemblies for soybean.
Babu Valliyodan,Babu Valliyodan,Steven B. Cannon,Philipp E. Bayer,Shengqiang Shu,Anne V. Brown,Longhui Ren,Jerry Jenkins,Claire Yik Lok Chung,Ting-Fung Chan,Christopher Daum,Christopher Plott,Alex Hastie,Kobi Baruch,Kerrie Barry,Wei Huang,Gunvant Patil,Rajeev K. Varshney,Haifei Hu,Jacqueline Batley,Yuxuan Yuan,Qijian Song,Robert M. Stupar,David Goodstein,Gary Stacey,Hon-Ming Lam,Scott A. Jackson,Jeremy Schmutz,Jane Grimwood,David Edwards,Henry T. Nguyen +30 more
TL;DR: The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for soybean's domestication and improvement, serving as a basis for future research and crop improvement efforts for this important crop species.
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