De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope.
Hippotragus equinus
de novo genome assembly
10X Genomics Chromium
Bovidae
genomic diversity
roan antelope
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
09 02 2021
09 02 2021
Historique:
received:
12
10
2020
accepted:
17
12
2021
entrez:
19
2
2021
pubmed:
20
2
2021
medline:
7
7
2021
Statut:
ppublish
Résumé
Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.
Identifiants
pubmed: 33604669
pii: 6114458
doi: 10.1093/g3journal/jkab002
pmc: PMC8022987
pii:
doi:
Banques de données
figshare
['10.25387/g3.13378799']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
Références
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12855-60
pubmed: 19625614
BMC Genomics. 2006 Aug 01;7:194
pubmed: 16882342
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
pubmed: 15961478
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Trends Ecol Evol. 2015 Feb;30(2):78-87
pubmed: 25534246
Genetica. 2011 May;139(5):617-38
pubmed: 21234647
Nucleic Acids Res. 2004 Mar 29;32(6):e56
pubmed: 15054124
Mol Ecol. 1999 Feb;8(2):227-38
pubmed: 10065541
Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13578-84
pubmed: 16938852
Nucleic Acids Res. 2018 Nov 30;46(21):e126
pubmed: 30107434
Genome Res. 2002 Aug;12(8):1269-76
pubmed: 12176934
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15758-63
pubmed: 24019490
Genome Biol. 2018 Sep 11;19(1):131
pubmed: 30205843
BMC Genomics. 2010 Nov 19;11:645
pubmed: 21092105
Nucleic Acids Res. 2008 Apr;36(7):2284-94
pubmed: 18287116
Gigascience. 2017 Apr 1;6(4):1-5
pubmed: 28327911
Genome Res. 2019 Apr;29(4):576-589
pubmed: 30760546
Bioinformatics. 2012 Dec 15;28(24):3326-8
pubmed: 23060615
Genome Res. 2017 May;27(5):757-767
pubmed: 28381613
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Biol Rev Camb Philos Soc. 2005 May;80(2):269-302
pubmed: 15921052
Zool Res. 2019 Nov 18;40(6):476-487
pubmed: 31592581
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Mol Ecol. 2004 Jul;13(7):1771-84
pubmed: 15189202
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
BMC Evol Biol. 2013 Aug 08;13:166
pubmed: 23927069
Bioinformatics. 2016 Jan 15;32(2):292-4
pubmed: 26428292
PLoS One. 2018 Mar 14;13(3):e0193588
pubmed: 29538441
Science. 2019 Jun 21;364(6446):
pubmed: 31221828
Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448
pubmed: 20516186
Biotechniques. 2012 Feb;52(2):87-94
pubmed: 22313406
Evol Appl. 2016 Oct 23;9(10):1205-1218
pubmed: 27877200
G3 (Bethesda). 2019 Jun 5;9(6):1785-1793
pubmed: 31000506
Nucleic Acids Res. 2012 Jan;40(1):e3
pubmed: 22021376
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Genome Biol. 2009;10(4):R42
pubmed: 19393038
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Science. 2009 Apr 24;324(5926):522-8
pubmed: 19390049
Mol Ecol Resour. 2011 Nov;11(6):1082-92
pubmed: 21791033
Gigascience. 2019 Aug 1;8(8):
pubmed: 31367745
Methods Mol Biol. 2019;1910:177-207
pubmed: 31278665
Sci Rep. 2018 Sep 26;8(1):14407
pubmed: 30258087
BMC Genomics. 2020 Mar 2;21(1):193
pubmed: 32122303
Nat Rev Genet. 2010 Oct;11(10):697-709
pubmed: 20847747
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Chromosome Res. 2015 Sep;23(3):415-20
pubmed: 26514350
PLoS One. 2011;6(6):e21400
pubmed: 21731731
Nat Commun. 2013;4:1858
pubmed: 23673643
Genes (Basel). 2019 Oct 25;10(11):
pubmed: 31717707
IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56
pubmed: 24091398
Mol Ecol Resour. 2020 Nov;20(6):1668-1681
pubmed: 32365406
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33
pubmed: 25431634
Nucleic Acids Res. 2017 Jan 4;45(D1):D744-D749
pubmed: 27899580
Trends Genet. 2018 Sep;34(9):666-681
pubmed: 29941292
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Evol Appl. 2020 Apr 27;13(8):2143-2154
pubmed: 32908610
Mol Ecol Resour. 2019 Nov;19(6):1578-1592
pubmed: 31484222
Gigascience. 2020 May 1;9(5):
pubmed: 32396200
Zoo Biol. 2019 Jan;38(1):106-118
pubmed: 30465726
Chromosome Res. 2018 Mar;26(1-2):25-43
pubmed: 29392473
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93
pubmed: 26582926