Third Report on Chicken Genes and Chromosomes 2015

Citation

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning D, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux P, Schmidt CJ, Schneider A, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D & Zhou H (2015) Third Report on Chicken Genes and Chromosomes 2015. Cytogenetic and Genome Research, 145 (2), pp. 78-179. https://doi.org/10.1159/000430927

Abstract
Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned. The chicken has long been a model organism for genetic and developmental studies and now takes its place as a model genome, opening up the fields of phylogenetics and comparative genomics like never before. This report summarizes the current efforts to complete the gaps in the genome and describes the progress of genomic annotation, particularly with respect to noncoding RNAs and genetic variants. Reviews of comparative genomics, avian evolution and sex determination are also given. Transcriptomic case studies are described as are developments in epigenetic studies. We also report on the development of the National Avian Research Facility (http://www.narf.ac.uk/) which is home to various chicken resources including antibodies, chicken lines and transgenic protocols and which hosts information currently available on the sequenced avian genomes.

Keywords
Genetics (clinical); Genetics; Molecular Biology

Notes
Additional co-authors: 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, 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
Cytogenetic and Genome Research: Volume 145, Issue 2