Literature DB >> 22293439

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'hom, Arkhat Abzhanov, Shane C Burgess, Amanda M Cooksey, Todd A Castoe, Nicholas G Crawford, Llewellyn D Densmore, Jennifer C Drew, Scott V Edwards, Brant C Faircloth, Matthew K Fujita, Matthew J Greenwold, Federico G Hoffmann, Jonathan M Howard, Taisen Iguchi, Daniel E Janes, Shahid Yar Khan, Satomi Kohno, Ap Jason de Koning, Stacey L Lance, Fiona M McCarthy, John E McCormack, Mark E Merchant, Daniel G Peterson, David D Pollock, Nader Pourmand, Brian J Raney, Kyria A Roessler, Jeremy R Sanford, Roger H Sawyer, Carl J Schmidt, Eric W Triplett, Tracey D Tuberville, Miryam Venegas-Anaya, Jason T Howard, Erich D Jarvis, Louis J Guillette, Travis C Glenn, Richard E Green, David A Ray.   

Abstract

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Entities:  

Mesh：

Year:  2012        PMID： 22293439      PMCID： PMC3334581          DOI： 10.1186/gb-2012-13-1-415

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  68 in total

1.  Nuclear DNA content and genome size of trout and human.

Authors:  J Dolezel; J Bartos; H Voglmayr; J Greilhuber
Journal:  Cytometry A       Date:  2003-02       Impact factor: 4.355

2.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Authors:  Mario Stanke; Mark Diekhans; Robert Baertsch; David Haussler
Journal:  Bioinformatics       Date:  2008-01-24       Impact factor: 6.937

3.  MicroRNAs support a turtle + lizard clade.

Authors:  Tyler R Lyson; Erik A Sperling; Alysha M Heimberg; Jacques A Gauthier; Benjamin L King; Kevin J Peterson
Journal:  Biol Lett       Date:  2011-07-20       Impact factor: 3.703

4.  Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Authors:  Ali Mortazavi; Erich M Schwarz; Brian Williams; Lorian Schaeffer; Igor Antoshechkin; Barbara J Wold; Paul W Sternberg
Journal:  Genome Res       Date:  2010-10-27       Impact factor: 9.043

5.  The sequence and de novo assembly of the giant panda genome.

Authors:  Ruiqiang Li; Wei Fan; Geng Tian; Hongmei Zhu; Lin He; Jing Cai; Quanfei Huang; Qingle Cai; Bo Li; Yinqi Bai; Zhihe Zhang; Yaping Zhang; Wen Wang; Jun Li; Fuwen Wei; Heng Li; Min Jian; Jianwen Li; Zhaolei Zhang; Rasmus Nielsen; Dawei Li; Wanjun Gu; Zhentao Yang; Zhaoling Xuan; Oliver A Ryder; Frederick Chi-Ching Leung; Yan Zhou; Jianjun Cao; Xiao Sun; Yonggui Fu; Xiaodong Fang; Xiaosen Guo; Bo Wang; Rong Hou; Fujun Shen; Bo Mu; Peixiang Ni; Runmao Lin; Wubin Qian; Guodong Wang; Chang Yu; Wenhui Nie; Jinhuan Wang; Zhigang Wu; Huiqing Liang; Jiumeng Min; Qi Wu; Shifeng Cheng; Jue Ruan; Mingwei Wang; Zhongbin Shi; Ming Wen; Binghang Liu; Xiaoli Ren; Huisong Zheng; Dong Dong; Kathleen Cook; Gao Shan; Hao Zhang; Carolin Kosiol; Xueying Xie; Zuhong Lu; Hancheng Zheng; Yingrui Li; Cynthia C Steiner; Tommy Tsan-Yuk Lam; Siyuan Lin; Qinghui Zhang; Guoqing Li; Jing Tian; Timing Gong; Hongde Liu; Dejin Zhang; Lin Fang; Chen Ye; Juanbin Zhang; Wenbo Hu; Anlong Xu; Yuanyuan Ren; Guojie Zhang; Michael W Bruford; Qibin Li; Lijia Ma; Yiran Guo; Na An; Yujie Hu; Yang Zheng; Yongyong Shi; Zhiqiang Li; Qing Liu; Yanling Chen; Jing Zhao; Ning Qu; Shancen Zhao; Feng Tian; Xiaoling Wang; Haiyin Wang; Lizhi Xu; Xiao Liu; Tomas Vinar; Yajun Wang; Tak-Wah Lam; Siu-Ming Yiu; Shiping Liu; Hemin Zhang; Desheng Li; Yan Huang; Xia Wang; Guohua Yang; Zhi Jiang; Junyi Wang; Nan Qin; Li Li; Jingxiang Li; Lars Bolund; Karsten Kristiansen; Gane Ka-Shu Wong; Maynard Olson; Xiuqing Zhang; Songgang Li; Huanming Yang; Jian Wang; Jun Wang
Journal:  Nature       Date:  2009-12-13       Impact factor: 49.962

6.  Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Authors:  Rami A Dalloul; Julie A Long; Aleksey V Zimin; Luqman Aslam; Kathryn Beal; Le Ann Blomberg; Pascal Bouffard; David W Burt; Oswald Crasta; Richard P M A Crooijmans; Kristal Cooper; Roger A Coulombe; Supriyo De; Mary E Delany; Jerry B Dodgson; Jennifer J Dong; Clive Evans; Karin M Frederickson; Paul Flicek; Liliana Florea; Otto Folkerts; Martien A M Groenen; Tim T Harkins; Javier Herrero; Steve Hoffmann; Hendrik-Jan Megens; Andrew Jiang; Pieter de Jong; Pete Kaiser; Heebal Kim; Kyu-Won Kim; Sungwon Kim; David Langenberger; Mi-Kyung Lee; Taeheon Lee; Shrinivasrao Mane; Guillaume Marcais; Manja Marz; Audrey P McElroy; Thero Modise; Mikhail Nefedov; Cédric Notredame; Ian R Paton; William S Payne; Geo Pertea; Dennis Prickett; Daniela Puiu; Dan Qioa; Emanuele Raineri; Magali Ruffier; Steven L Salzberg; Michael C Schatz; Chantel Scheuring; Carl J Schmidt; Steven Schroeder; Stephen M J Searle; Edward J Smith; Jacqueline Smith; Tad S Sonstegard; Peter F Stadler; Hakim Tafer; Zhijian Jake Tu; Curtis P Van Tassell; Albert J Vilella; Kelly P Williams; James A Yorke; Liqing Zhang; Hong-Bin Zhang; Xiaojun Zhang; Yang Zhang; Kent M Reed
Journal:  PLoS Biol       Date:  2010-09-07       Impact factor: 8.029

7.  Antibacterial properties of serum from the American alligator (Alligator mississippiensis).

Authors:  Mark E Merchant; Cherie Roche; Ruth M Elsey; Jan Prudhomme
Journal:  Comp Biochem Physiol B Biochem Mol Biol       Date:  2003-11       Impact factor: 2.231

8.  Origin of avian genome size and structure in non-avian dinosaurs.

Authors:  Chris L Organ; Andrew M Shedlock; Andrew Meade; Mark Pagel; Scott V Edwards
Journal:  Nature       Date:  2007-03-08       Impact factor: 49.962

9.  Ensembl 2011.

Authors:  Paul Flicek; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Yuan Chen; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Leo Gordon; Maurice Hendrix; Thibaut Hourlier; Nathan Johnson; Andreas Kähäri; Damian Keefe; Stephen Keenan; Rhoda Kinsella; Felix Kokocinski; Eugene Kulesha; Pontus Larsson; Ian Longden; William McLaren; Bert Overduin; Bethan Pritchard; Harpreet Singh Riat; Daniel Rios; Graham R S Ritchie; Magali Ruffier; Michael Schuster; Daniel Sobral; Giulietta Spudich; Y Amy Tang; Stephen Trevanion; Jana Vandrovcova; Albert J Vilella; Simon White; Steven P Wilder; Amonida Zadissa; Jorge Zamora; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Ian Dunham; Richard Durbin; Xosé M Fernández-Suarez; Javier Herrero; Tim J P Hubbard; Anne Parker; Glenn Proctor; Jan Vogel; Stephen M J Searle
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

10.  A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization.

Authors:  Xueyan Shan; David A Ray; John A Bunge; Daniel G Peterson
Journal:  BMC Genomics       Date:  2009-07-14       Impact factor: 3.969
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  61 in total

1.  Evolution of MHC class I in the order Crocodylia.

Authors:  Weerachai Jaratlerdsiri; Sally R Isberg; Damien P Higgins; Simon Y W Ho; Jan Salomonsen; Karsten Skjodt; Lee G Miles; Jaime Gongora
Journal:  Immunogenetics       Date:  2013-11-20       Impact factor: 2.846

2.  Major histocompatibility complex genes and locus organization in the Komodo dragon (Varanus komodoensis).

Authors:  Kent M Reed; Robert E Settlage
Journal:  Immunogenetics       Date:  2021-05-12       Impact factor: 2.846

3.  Evolution of V genes from the TRV loci of mammals.

Authors:  David N Olivieri; Santiago Gambón-Cerdá; Francisco Gambón-Deza
Journal:  Immunogenetics       Date:  2015-05-31       Impact factor: 2.846

4.  A critical appraisal of the use of microRNA data in phylogenetics.

Authors:  Robert C Thomson; David C Plachetzki; D Luke Mahler; Brian R Moore
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-28       Impact factor: 11.205

5.  Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development.

Authors:  Weier Bao; Matthew J Greenwold; Roger H Sawyer
Journal:  Gene       Date:  2016-06-15       Impact factor: 3.688

Review 6.  Studying mechanisms of regeneration in amphibian and reptilian vertebrate models.

Authors:  Kenro Kusumi; Rebecca E Fisher
Journal:  Anat Rec (Hoboken)       Date:  2012-08-29       Impact factor: 2.064

7.  Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles.

Authors:  Daniel J Field; Jacques A Gauthier; Benjamin L King; Davide Pisani; Tyler R Lyson; Kevin J Peterson
Journal:  Evol Dev       Date:  2014-05-05       Impact factor: 1.930

8.  Intense and specialized dendritic localization of the fragile X mental retardation protein in binaural brainstem neurons: a comparative study in the alligator, chicken, gerbil, and human.

Authors:  Yuan Wang; Hitomi Sakano; Karisa Beebe; Maile R Brown; Rian de Laat; Mark Bothwell; Randy J Kulesza; Edwin W Rubel
Journal:  J Comp Neurol       Date:  2014-06-15       Impact factor: 3.215

9.  Sex-biased expression of sex-differentiating genes FOXL2 and FGF9 in American alligators, alligator Mississippiensis.

Authors:  D E Janes; R M Elsey; E M Langan; N Valenzuela; S V Edwards
Journal:  Sex Dev       Date:  2013-05-08       Impact factor: 1.824

10.  Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).

Authors:  Ylenia Chiari; Vincent Cahais; Nicolas Galtier; Frédéric Delsuc
Journal:  BMC Biol       Date:  2012-07-27       Impact factor: 7.431
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