Improved reference genome for the domestic horse increases assembly contiguity and composition

被引：160

作者：

Kalbfleisch, Theodore S. ^{[1
]}

Rice, Edward S. ^{[2
]}

DePriest, Michael S., Jr. ^{[1
]}

Walenz, Brian P. ^{[3
]}

Hestand, Matthew S. ^{[4
]}

Vermeesch, Joris R. ^{[4
]}

O'Connell, Brendan L. ^{[2
,16
]}

Fiddes, Ian T. ^{[2
,5
]}

Vershinina, Alisa O. ^{[6
]}

Saremi, Nedda F. ^{[2
]}

Petersen, Jessica L. ^{[7
]}

Finno, Carrie J. ^{[8
]}

Bellone, Rebecca R. ^{[8
,9
]}

McCue, Molly E. ^{[10
]}

Brooks, Samantha A. ^{[11
]}

Bailey, Ernest ^{[12
]}

Orlando, Ludovic ^{[13
,14
]}

Greene, Richard E. ^{[2
]}

Miller, Donald C. ^{[15
]}

Antczak, Douglas F. ^{[15
]}

MacLeod, James N. ^{[12
]}

机构：

[1] Univ Louisville, Sch Med, Dept Biochem & Mol Genet, Louisville, KY 40292 USA

[2] UC Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

[3] NHGRI, Genome Informat Sect, Computat & Stat Genom Branch, NIH, Bethesda, MD 20892 USA

[4] Katholieke Univ Leuven, Ctr Human Genet, B-3000 Leuven, Belgium

[5] 10x Genomics Inc, Pleasanton, CA 94566 USA

[6] UC Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA

[7] Univ Nebraska, Dept Anim Sci, Lincoln, NE 68583 USA

[8] Univ Calif Davis, Dept Populat Hlth & Reprod, Davis, CA 95616 USA

[9] Univ Calif Davis, Vet Genet Lab, Davis, CA 95616 USA

[10] Univ Minnesota, Dept Vet Populat Med, St Paul, MN 55108 USA

[11] Univ Florida, UF Genet Inst, Dept Anim Sci, Gainesville, FL 32611 USA

[12] Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA

[13] Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark

[14] Univ Toulouse, Univ Paul Sabatier, Lab Anthropobiol Mol & Imagerie Synth, CNRS,UMR 5288, Toulouse, France

[15] Cornell Univ, Coll Vet Med, Baker Inst Anim Hlth, Ithaca, NY 14853 USA

[16] Oregon Hlth & Sci Univ, Med & Mol Genet, Portland, OR 97239 USA

来源：

COMMUNICATIONS BIOLOGY | 2018年 / 1卷

基金：

美国国家卫生研究院;

关键词：

READ ALIGNMENT; MESSENGER-RNA; SEQUENCE; ANNOTATION; GENES;

D O I：

10.1038/s42003-018-0199-z

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

引用

页数：8

共 54 条

[41] Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion [J].

Sarkar, Sanjay ;

Bailey, Ernest ;

Go, Yun Young ;

Cook, R. Frank ;

Kalbfleisch, Ted ;

Eberth, John ;

Chelvarajan, R. Lakshman ;

Shuck, Kathleen M. ;

Artiushin, Sergey ;

Timoney, Peter J. ;

Balasuriya, Udeni B. R. .

PLOS GENETICS, 2016, 12 (12)

[42] Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds [J].

Schaefer, Robert J ;

Schubert, Mikkel K ;

Bailey, Ernest K ;

Bannasch, Danika L ;

Barrey, Eric P ;

Bar-Gal, Gila Kahila ;

Brem, Gottfried J ;

Brooks, Samantha A ;

Distl, Ottmar K ;

Fries, Ruedi K ;

Finno, Carrie J ;

Gerber, Vinzenz K ;

Haase, Bianca K ;

Jagannathan, Vidhya K ;

Kalbfleisch, Ted K ;

Leeb, Tosso K ;

Lindgren, Gabriella K ;

Lopes, Maria Susana ;

Mach, Nuria K ;

Machado, Artur daCamara ;

MacLeod, James N ;

McCoy, Annette K ;

Metzger, Julia K ;

Penedo, Cecilia K ;

Polani, Sagi K ;

Rieder, Stefan K ;

Tammen, Imke K ;

Tetens, Jens K ;

Thaller, Georg P ;

Verini-Supplizi, Andrea P ;

Wade, Claire M ;

Wallner, Barbara T ;

Orlando, Ludovic S ;

Mickelson, James R ;

McCue, Molly E .

BMC GENOMICS, 2017, 18

[43] Quality control and preprocessing of metagenomic datasets [J].

Schmieder, Robert ;

Edwards, Robert .

BIOINFORMATICS, 2011, 27 (06) :863-864

[44] AdapterRemoval v2: Rapid adapter trimming, identification, and read merging [J].

Schubert M. ;

Lindgreen S. ;

Orlando L. .

BMC Research Notes, 9 (1)

[45] Prehistoric genomes reveal the genetic foundation and cost of horse domestication [J].

Schubert, Mikkel ;

Jonsson, Hakon ;

Chang, Dan ;

Sarkissian, Clio Der ;

Ermini, Luca ;

Ginolhac, Aurelien ;

Albrechtsen, Anders ;

Dupanloup, Isabelle ;

Foucal, Adrien ;

Petersen, Bent ;

Fumagalli, Matteo ;

Raghavan, Maanasa ;

Seguin-Orlando, Andaine ;

Korneliussen, Thorfinn S. ;

Velazquez, Amhed M. V. ;

Stenderup, Jesper ;

Hoover, Cindi A. ;

Rubin, Carl-Johan ;

Alfarhan, Ahmed H. ;

Alquraishi, Saleh A. ;

Al-Rasheid, Khaled A. S. ;

MacHugh, David E. ;

Kalbfleisch, Ted ;

MacLeod, James N. ;

Rubin, Edward M. ;

Sicheritz-Ponten, Thomas ;

Andersson, Leif ;

Hofreiter, Michael ;

Marques-Bonet, Tomas ;

Gilbert, M. Thomas P. ;

Nielsen, Rasmus ;

Excoffier, Laurent ;

Willerslev, Eske ;

Shapiro, Beth ;

Orlando, Ludovic .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (52) :E5661-E5669

[46] BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs [J].

Simao, Felipe A. ;

Waterhouse, Robert M. ;

Ioannidis, Panagiotis ;

Kriventseva, Evgenia V. ;

Zdobnov, Evgeny M. .

BIOINFORMATICS, 2015, 31 (19) :3210-3212

[47] Host genetic influence on papillomavirus-induced tumors in the horse [J].

Staiger, Elizabeth A. ;

Tseng, Chia T. ;

Miller, Donald ;

Cassano, Jennifer M. ;

Nasir, Lubna ;

Garrick, Dorian ;

Brooks, Samantha A. ;

Antczak, Douglas F. .

INTERNATIONAL JOURNAL OF CANCER, 2016, 139 (04) :784-792

[48] Brother of CDO (BOC) expression in equine articular cartilage [J].

Vanderman, K. S. ;

Tremblay, M. ;

Zhu, W. ;

Shimojo, M. ;

Mienaltowski, M. J. ;

Coleman, S. J. ;

MacLeod, J. N. .

OSTEOARTHRITIS AND CARTILAGE, 2011, 19 (04) :435-438

[49] Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse [J].

Wade, C. M. ;

Giulotto, E. ;

Sigurdsson, S. ;

Zoli, M. ;

Gnerre, S. ;

Imsland, F. ;

Lear, T. L. ;

Adelson, D. L. ;

Bailey, E. ;

Bellone, R. R. ;

Bloecker, H. ;

Distl, O. ;

Edgar, R. C. ;

Garber, M. ;

Leeb, T. ;

Mauceli, E. ;

MacLeod, J. N. ;

Penedo, M. C. T. ;

Raison, J. M. ;

Sharpe, T. ;

Vogel, J. ;

Andersson, L. ;

Antczak, D. F. ;

Biagi, T. ;

Binns, M. M. ;

Chowdhary, B. P. ;

Coleman, S. J. ;

Della Valle, G. ;

Fryc, S. ;

Guerin, G. ;

Hasegawa, T. ;

Hill, E. W. ;

Jurka, J. ;

Kiialainen, A. ;

Lindgren, G. ;

Liu, J. ;

Magnani, E. ;

Mickelson, J. R. ;

Murray, J. ;

Nergadze, S. G. ;

Onofrio, R. ;

Pedroni, S. ;

Piras, M. F. ;

Raudsepp, T. ;

Rocchi, M. ;

Roed, K. H. ;

Ryder, O. A. ;

Searle, S. ;

Skow, L. ;

Swinburne, J. E. .

SCIENCE, 2009, 326 (5954) :865-867

[50] Figaro: a novel statistical method for vector sequence removal [J].

White, James Robert ;

Roberts, Michael ;

Yorke, James A. ;

Pop, Mihai .

BIOINFORMATICS, 2008, 24 (04) :462-467

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