One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
27 07 2020
27 07 2020
Historique:
accepted:
18
05
2020
revised:
16
04
2020
received:
17
01
2020
pubmed:
4
6
2020
medline:
24
9
2020
entrez:
4
6
2020
Statut:
ppublish
Résumé
A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for small organisms or precious samples. Here we demonstrate the feasibility of creating a chromosome scale assembly using a hybrid method for a low input sample, a single outbred Drosophila melanogaster. Our approach combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long range scaffolding. This single fly genome assembly has a N50 of 26 Mb, a length that encompasses entire chromosome arms, contains 95% of expected single copy orthologs, and a nearly complete assembly of this individual's Wolbachia endosymbiont. The methods described here enable the accurate and complete assembly of genomes from small, field collected organisms as well as precious clinical samples.
Identifiants
pubmed: 32491177
pii: 5850803
doi: 10.1093/nar/gkaa450
pmc: PMC7367183
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e75Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM128932
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM133569
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG008345
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Am J Hum Genet. 2013 Aug 8;93(2):278-88
pubmed: 23910464
Genome Res. 2017 May;27(5):801-812
pubmed: 27940952
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Trends Biotechnol. 2017 Jun;35(6):547-558
pubmed: 28284542
Annu Rev Anim Biosci. 2019 Feb 15;7:17-40
pubmed: 30485757
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9726-9731
pubmed: 30201725
Genetics. 2019 Dec;213(4):1495-1511
pubmed: 31666292
Nat Commun. 2019 Jan 2;10(1):4
pubmed: 30602775
Nat Genet. 2018 Jan;50(1):20-25
pubmed: 29255259
Genetics. 2015 Apr;199(4):1229-41
pubmed: 25631317
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Microbiologyopen. 2016 Dec;5(6):923-936
pubmed: 27461737
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Exp Cell Res. 2017 Sep 15;358(2):433-438
pubmed: 28017728
J Insect Physiol. 2019 May - Jun;115:33-39
pubmed: 30953618
Genes (Basel). 2019 Jan 18;10(1):
pubmed: 30669388
Curr Top Dev Biol. 2019;135:315-351
pubmed: 31155362
Insect Mol Biol. 2019 Dec;28(6):739-758
pubmed: 31120160
Nucleic Acids Res. 2016 Nov 2;44(19):e147
pubmed: 27458204
J Exp Zool. 1948 Aug;108(3):327-35
pubmed: 18882503
Methods. 2012 Nov;58(3):268-76
pubmed: 22652625
PLoS One. 2011;6(8):e23501
pubmed: 21876754
G3 (Bethesda). 2015 Feb 11;5(4):593-603
pubmed: 25673134
Nat Methods. 2020 Feb;17(2):155-158
pubmed: 31819265
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Science. 2000 Mar 24;287(5461):2185-95
pubmed: 10731132
Gigascience. 2019 Oct 1;8(10):
pubmed: 31609423
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
PLoS Genet. 2017 Jan 3;13(1):e1006529
pubmed: 28045893
Nat Rev Genet. 2011 Nov 29;13(1):36-46
pubmed: 22124482
Nat Commun. 2019 Oct 3;10(1):4485
pubmed: 31582763
Mol Ecol. 2017 Mar;26(6):1465-1476
pubmed: 28001319
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nature. 2011 Jul 13;475(7357):493-6
pubmed: 21753753
Genome Res. 2016 Mar;26(3):342-50
pubmed: 26848124
Annu Rev Entomol. 2018 Jan 7;63:31-45
pubmed: 28938083