tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TLDR
A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.Abstract:
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.read more
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The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
Shaogui Guo,Shaogui Guo,Jianguo Zhang,Jianguo Zhang,Honghe Sun,Honghe Sun,Jérôme Salse,William J. Lucas,Haiying Zhang,Yi Zheng,Linyong Mao,Yi Ren,Zhiwen Wang,Jiumeng Min,Xiaosen Guo,Florent Murat,Byung-Kook Ham,Zhaoliang Zhang,Shan Gao,Mingyun Huang,Yimin Xu,Silin Zhong,Aureliano Bombarely,Lukas A. Mueller,Hong Zhao,Hongju He,Yan Zhang,Zhonghua Zhang,Sanwen Huang,Tao Tan,Erli Pang,Kui Lin,Qun Hu,Hanhui Kuang,Peixiang Ni,Peixiang Ni,Bo Wang,Jingan Liu,Qinghe Kou,Wenju Hou,Xiaohua Zou,Jiao Jiang,Guoyi Gong,Kathrin Klee,Heiko Schoof,Ying Huang,Xuesong Hu,Shanshan Dong,Dequan Liang,Juan Wang,Kui Wu,Yang Xia,Xiang Zhao,Zequn Zheng,Miao Xing,Xinming Liang,Bangqing Huang,Tian Lv,Junyi Wang,Ye Yin,Hongping Yi,Ruiqiang Li,Mingzhu Wu,Amnon Levi,Xingping Zhang,James J. Giovannoni,James J. Giovannoni,Jun Wang,Jun Wang,Yunfu Li,Zhangjun Fei,Zhangjun Fei,Yong Xu +72 more
TL;DR: A high-quality draft genome sequence of the east Asia watermelon cultivar 97103 containing 23,440 predicted protein-coding genes is reported, which yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits.
Journal ArticleDOI
Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells
Esen Sefik,Naama Geva-Zatorsky,Sungwhan F. Oh,Liza Konnikova,David Zemmour,Abigail Manson McGuire,Dalia Burzyn,Adriana Ortiz-Lopez,Mercedes Lobera,Jianfei Yang,Shomir Ghosh,Ashlee M. Earl,Scott B. Snapper,Ray Jupp,Dennis L. Kasper,Diane Mathis,Diane Mathis,Christophe Benoist,Christophe Benoist +18 more
TL;DR: It is reported that symbiotic members of the human gut microbiota induce a distinct Treg population in the mouse colon, which constrains immuno-inflammatory responses.
Journal ArticleDOI
Genome Structure of the Legume, Lotus japonicus
Shusei Sato,Yasukazu Nakamura,Takakazu Kaneko,Erika Asamizu,Tomohiko Kato,Mitsuteru Nakao,Shigemi Sasamoto,Akiko Watanabe,Akiko Ono,Kumiko Kawashima,Tsunakazu Fujishiro,Midori Katoh,Mitsuyo Kohara,Yoshie Kishida,Chiharu Minami,Shinobu Nakayama,Naomi Nakazaki,Yoshimi Shimizu,Sayaka Shinpo,Chika Takahashi,Tsuyuko Wada,Manabu Yamada,Nobuko Ohmido,Makoto Hayashi,Kiichi Fukui,Tomoya Baba,Tomoko Nakamichi,Hirotada Mori,Satoshi Tabata +28 more
TL;DR: Structural features of the L. japonicus genome are reported, providing the first opportunity to look into the complex and unique genetic system of legumes.
Journal ArticleDOI
The genome of a motile marine Synechococcus
Brian Palenik,B. Brahamsha,Frank W. Larimer,Frank W. Larimer,Miriam Land,Miriam Land,Loren Hauser,Loren Hauser,Patrick S. G. Chain,Patrick S. G. Chain,Jane Lamerdin,Jane Lamerdin,Warren Regala,Warren Regala,Eric E. Allen,Eric E. Allen,Jay McCarren,Ian T. Paulsen,Alexis Dufresne,Frédéric Partensky,Eric A. Webb,John B. Waterbury +21 more
TL;DR: The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages, and is more of a generalist than two related marine cyanobacteria.
Journal ArticleDOI
DNA sequence and analysis of human chromosome 9
Andrew J. Mungall,Sophie Palmer,Sarah Sims,C A Edwards,Jennifer L. Ashurst,Laurens G. Wilming,Matthew Jones,Roger Horton,Sarah E. Hunt,Carol Scott,James G. R. Gilbert,Michele Clamp,Graeme Bethel,Sarah Milne,R Ainscough,J P Almeida,K D Ambrose,T D Andrews,R I S Ashwell,A K Babbage,C L Bagguley,J Bailey,Ruby Banerjee,Darren Barker,K F Barlow,K Bates,David Beare,Helen Beasley,O. Beasley,Christine P. Bird,S. Blakey,S Bray-Allen,J Brook,A J Brown,J Y Brown,D C Burford,W Burrill,John Burton,C Carder,Nigel P. Carter,J C Chapman,S Y Clark,Graeme T Clark,C M Clee,S. M. Clegg,V. Cobley,R. E. Collier,Joanna Collins,L K Colman,N Corby,G. J. Coville,K M Culley,Pawandeep Dhami,Jim Davies,Matthew Dunn,M Earthrowl,A E Ellington,K A Evans,L M Faulkner,Matthew D. Francis,Adam Frankish,J Frankland,Lisa French,P Garner,J Garnett,Mohammed J. R. Ghori,L M Gilby,Christopher J. Gillson,Rebecca Glithero,Darren Grafham,M Grant,Susan M. Gribble,C Griffiths,Mark Griffiths,Rebekah Hall,K S Halls,S Hammond,Joanna Harley,E. Hart,Paul Heath,R Heathcott,S. Holmes,Philip Howden,Kevin L. Howe,Gareth R. Howell,Elizabeth J. Huckle,Sean Humphray,Matthew Humphries,Adrienne Hunt,Christopher M. Johnson,A Joy,M. Kay,Stephen Keenan,A M Kimberley,A. King,Gavin K. Laird,Cordelia Langford,S Lawlor,Daniel Leongamornlert,Margaret A. Leversha,Christine Lloyd,D. M. Lloyd,Jane E. Loveland,J Lovell,Sancha Martin,M Mashreghi-Mohammadi,Gareth Maslen,Lucy Matthews,O. T. McCann,S J McLaren,Kirsten McLay,Amanda McMurray,M. J F Moore,James C. Mullikin,David Niblett,T Nickerson,K L Novik,Karen Oliver,E K Overton-Larty,Anne Parker,R Patel,A. V. Pearce,A I Peck,Benjamin Phillimore,Sam Phillips,Robert W. Plumb,K M Porter,Y. Ramsey,S A Ranby,Catherine M. Rice,Mark T. Ross,S. Searle,Harminder Sehra,E Sheridan,C. D. Skuce,Sarah E. Smith,Michelle Smith,L Spraggon,S. Squares,Charles A. Steward,N Sycamore,G Tamlyn-Hall,J Tester,A J Theaker,Duncan W. Thomas,A Thorpe,Alan Tracey,A Tromans,B Tubby,Melanie M. Wall,J. M. Wallis,Anthony P. West,S S White,S. Whitehead,H Whittaker,A Wild,Dave Willey,T. E. Wilmer,Jonathan Wood,Paul Wray,J C Wyatt,L Young,R M Younger,David R. Bentley,Alan Coulson,Richard Durbin,Tim Hubbard,John Sulston,Ian Dunham,Jane Rogers,Stephan Beck +170 more
TL;DR: Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block, and detects recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
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