BACKGROUND: The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. RESULTS: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. CONCLUSIONS: Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.
n class="abstract_title">BACKGROUND: The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. RESULTS: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. CONCLUSIONS: Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.
Authors: W James Kent; Robert Baertsch; Angie Hinrichs; Webb Miller; David Haussler Journal: Proc Natl Acad Sci U S A Date: 2003-09-19 Impact factor: 11.205
Authors: Christian Geier; Andreas Perrot; Cemil Ozcelik; Priska Binner; Damian Counsell; Katrin Hoffmann; Bernhard Pilz; Yvonne Martiniak; Katja Gehmlich; Peter F M van der Ven; Dieter O Fürst; Arnold Vornwald; Eberhard von Hodenberg; Peter Nürnberg; Thomas Scheffold; Rainer Dietz; Karl Josef Osterziel Journal: Circulation Date: 2003-03-18 Impact factor: 29.690
Authors: Scott Schwartz; W James Kent; Arian Smit; Zheng Zhang; Robert Baertsch; Ross C Hardison; David Haussler; Webb Miller Journal: Genome Res Date: 2003-01 Impact factor: 9.043
Authors: Michael Schmid; Jacqueline Smith; David W Burt; Bronwen L Aken; Parker B Antin; Alan L Archibald; Chris Ashwell; Perry J Blackshear; Clarissa Boschiero; C Titus Brown; Shane C Burgess; Hans H Cheng; William Chow; Derrick J Coble; Amanda Cooksey; Richard P M A Crooijmans; Joana Damas; Richard V N Davis; Dirk-Jan de Koning; Mary E Delany; Thomas Derrien; Takele T Desta; Ian C Dunn; Matthew Dunn; Hans Ellegren; Lél Eöry; Ionas Erb; Marta Farré; Mario Fasold; Damarius Fleming; Paul Flicek; Katie E Fowler; Laure Frésard; David P Froman; Valerie Garceau; Paul P Gardner; Almas A Gheyas; Darren K Griffin; Martien A M Groenen; Thomas Haaf; Olivier Hanotte; Alan Hart; Julien Häsler; S Blair Hedges; Jana Hertel; Kerstin Howe; Allen Hubbard; David A Hume; Pete Kaiser; Darek Kedra; Stephen J Kemp; Christophe Klopp; Kalmia E Kniel; Richard Kuo; Sandrine Lagarrigue; Susan J Lamont; Denis M Larkin; Raman A Lawal; Sarah M Markland; Fiona McCarthy; Heather A McCormack; Marla C McPherson; Akira Motegi; Stefan A Muljo; Andrea Münsterberg; Rishi Nag; Indrajit Nanda; Michael Neuberger; Anne Nitsche; Cedric Notredame; Harry Noyes; Rebecca O'Connor; Elizabeth A O'Hare; Andrew J Oler; Sheila C Ommeh; Helio Pais; Michael Persia; Frédérique Pitel; Likit Preeyanon; Pablo Prieto Barja; Elizabeth M Pritchett; Douglas D Rhoads; Charmaine M Robinson; Michael N Romanov; Max Rothschild; Pierre-François Roux; Carl J Schmidt; Alisa-Sophia Schneider; Matthew G Schwartz; Steve M Searle; Michael A Skinner; Craig A Smith; Peter F Stadler; Tammy E Steeves; Claus Steinlein; Liang Sun; Minoru Takata; Igor Ulitsky; Qing Wang; Ying Wang; Wesley C Warren; Jonathan M D Wood; David Wragg; Huaijun Zhou Journal: Cytogenet Genome Res Date: 2015-07-14 Impact factor: 1.636