A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

被引：195

作者：

Warren, Wesley C. ^{[1
]}

Hillier, LaDeana W. ^{[1
]}

Tomlinson, Chad ^{[1
]}

Minx, Patrick ^{[1
]}

Kremitzki, Milinn ^{[1
]}

Graves, Tina ^{[1
]}

Markovic, Chris ^{[1
]}

Bouk, Nathan ^{[2
]}

Pruitt, Kim D. ^{[2
]}

Thibaud-Nissen, Francoise ^{[2
]}

Schneider, Valerie ^{[2
]}

Mansour, Tamer A. ^{[3
]}

Brown, C. Titus ^{[3
]}

Zimin, Aleksey ^{[4
]}

Hawken, Rachel ^{[5
]}

Abrahamsen, Mitch ^{[5
]}

Pyrkosz, Alexis B. ^{[6
]}

Morisson, Mireille ^{[7
]}

Fillon, Valerie ^{[7
]}

Vignal, Alain ^{[7
]}

Chow, William ^{[8
]}

Howe, Kerstin ^{[8
]}

Fulton, Janet E. ^{[9
]}

Miller, Marcia M. ^{[10
]}

Lovell, Peter ^{[11
]}

Mello, Claudio V. ^{[11
]}

Wirthlin, Morgan ^{[11
]}

Mason, Andrew S. ^{[12
,13
]}

Kuo, Richard ^{[12
,13
]}

Burt, David W. ^{[12
,13
]}

Dodgson, Jerry B. ^{[14
]}

Cheng, Hans H. ^{[6
]}

机构：

[1] Washington Univ, Sch Med, McDonnell Genome Inst, 4444 Forest Pk Blvd, St Louis, MO 63108 USA

[2] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

[3] Univ Calif Davis, Davis, CA 95616 USA

[4] Univ Maryland, Inst Phys Sci & Technol, College Pk, MD 20742 USA

[5] Cobb Vantress Inc, Siloam Springs, AR 72761 USA

[6] USDA ARS, Avian Dis & Oncol Lab, 3606 E Mt Hope Rd, E Lansing, MI 48823 USA

[7] Univ Toulouse, Genet Physiol & Syst Elevage, INRA, Auzeville Castanet Tolos, France

[8] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[9] Hy Line Int, Dallas, IA 50063 USA

[10] Beckman Res Inst, Duarte, CA 91010 USA

[11] Oregon Hlth & Sci Univ, Dept Behav Neurosci, Portland, OR 97239 USA

[12] Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland

[13] Univ Edinburgh, Royal Dick Sch Vet Studies, Roslin EH25 9RG, Midlothian, Scotland

[14] Michigan State Univ, Dept Microbiol & Mol Genet, E Lansing, MI 48824 USA

来源：

G3-GENES GENOMES GENETICS | 2017年 / 7卷 / 01期

基金：

美国农业部; 英国生物技术与生命科学研究理事会;

关键词：

Gallus gallus; genome assembly; MHC; LEUKOCYTE RECEPTOR COMPLEX; GENE; MAP; IDENTIFICATION; ALIGNMENT; SOFTWARE; RESOURCE; CHROMOSOMES; ANNOTATION; EXPANSION;

D O I：

10.1534/g3.116.035923

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.

引用

页码：109 / 117

页数：9

共 51 条

[1] At least one class I gene in restriction fragment pattern-Y (Rfp-Y), the second MHC gene cluster in the chicken, is transcribed, polymorphic, and shows divergent specialization in antigen binding region [J].

Afanassieff, M ;

Goto, RM ;

Ha, J ;

Sherman, MA ;

Zhong, LW ;

Auffray, C ;

Coudert, F ;

Zoorob, R ;

Miller, MM .

JOURNAL OF IMMUNOLOGY, 2001, 166 (05) :3324-3333

[2] Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition [J].

Bellott, Daniel W. ;

Skaletsky, Helen ;

Pyntikova, Tatyana ;

Mardis, Elaine R. ;

Graves, Tina ;

Kremitzki, Colin ;

Brown, Laura G. ;

Rozen, Steve ;

Warren, Wesley C. ;

Wilson, Richard K. ;

Page, David C. .

NATURE, 2010, 466 (7306) :612-U3

[3]

Berlin K., 2014, BIORXIV, V1, P1

[4] SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information [J].

Boetzer, Marten ;

Pirovano, Walter .

BMC BIOINFORMATICS, 2014, 15

[5]

Boutet E, 2016, METHODS MOL BIOL, V1374, P23, DOI 10.1007/978-1-4939-3167-5_2

[6] Gene: a gene-centered information resource at NCBI [J].

Brown, Garth R. ;

Hem, Vichet ;

Katz, Kenneth S. ;

Ovetsky, Michael ;

Wallin, Craig ;

Ermolaeva, Olga ;

Tolstoy, Igor ;

Tatusova, Tatiana ;

Pruitt, Kim D. ;

Maglott, Donna R. ;

Murphy, Terence D. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D36-D42

[7] Resolving the complexity of the human genome using single-molecule sequencing [J].

Chaisson, Mark J. P. ;

Huddleston, John ;

Dennis, Megan Y. ;

Sudmant, Peter H. ;

Malig, Maika ;

Hormozdiari, Fereydoun ;

Antonacci, Francesca ;

Surti, Urvashi ;

Sandstrom, Richard ;

Boitano, Matthew ;

Landolin, Jane M. ;

Stamatoyannopoulos, John A. ;

Hunkapiller, Michael W. ;

Korlach, Jonas ;

Eichler, Evan E. .

NATURE, 2015, 517 (7536) :608-U163

[8] High speed BLASTN: an accelerated MegaBLAST search tool [J].

Chen, Ying ;

Ye, Weicai ;

Zhang, Yongdong ;

Xu, Yuesheng .

NUCLEIC ACIDS RESEARCH, 2015, 43 (16) :7762-7768

[9] DEVELOPMENT OF A GENETIC-MAP OF THE CHICKEN WITH MARKERS OF HIGH UTILITY [J].

CHENG, HH ;

LEVIN, I ;

VALLEJO, RL ;

KHATIB, H ;

DODGSON, JB ;

CRITTENDEN, LB ;

HILLEL, J .

POULTRY SCIENCE, 1995, 74 (11) :1855-1874

[10] LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons [J].

Ellinghaus, David ;

Kurtz, Stefan ;

Willhoeft, Ute .

BMC BIOINFORMATICS, 2008, 9 (1)

← 1 2 3 4 5 6 →