A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.).
Hermetia illucens
BRAKER2
Black Soldier Fly
Hi-C assembly
PacBio
domestication
genome annotation
genome assembly
inbreeding
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
07 05 2021
07 05 2021
Historique:
received:
10
12
2020
accepted:
09
03
2021
pubmed:
19
3
2021
medline:
8
7
2021
entrez:
18
3
2021
Statut:
ppublish
Résumé
Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.
Identifiants
pubmed: 33734373
pii: 6178282
doi: 10.1093/g3journal/jkab085
pmc: PMC8104945
pii:
doi:
Banques de données
figshare
['10.25387/g3.14069669.']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M011194/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT207492
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9
pubmed: 26612867
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Genome Biol. 2020 Feb 7;21(1):30
pubmed: 32033565
Cell Res. 2020 Jan;30(1):50-60
pubmed: 31767972
F1000Res. 2018 Feb 5;7:
pubmed: 29568489
Gigascience. 2021 Jan 9;10(1):
pubmed: 33420778
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Curr Biol. 2002 Sep 17;12(18):1547-56
pubmed: 12372246
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Nucleic Acids Res. 2019 Jan 8;47(D1):D759-D765
pubmed: 30364959
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Methods Mol Biol. 2019;1962:65-95
pubmed: 31020555
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Hum Mol Genet. 2006 Mar 1;15(5):789-95
pubmed: 16436455
Gigascience. 2020 Feb 1;9(2):
pubmed: 32101299
J R Soc Interface. 2019 Feb 28;16(151):20180735
pubmed: 30958190
PLoS One. 2015 Dec 23;10(12):e0144601
pubmed: 26699129
Pest Manag Sci. 2001 Oct;57(10):958-67
pubmed: 11695190
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
J Chem Ecol. 2013 Sep;39(9):1232-45
pubmed: 24036972
Nucleic Acids Res. 2008 Jun;36(10):3420-35
pubmed: 18445632
Bioinformatics. 2018 Jan 15;34(2):353-360
pubmed: 29112732
Gigascience. 2019 Nov 1;8(11):
pubmed: 31682256
Gigascience. 2020 Jun 1;9(6):
pubmed: 32543654
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
J Clean Prod. 2019 Feb 20;211:303-308
pubmed: 30799911
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Proc Natl Acad Sci U S A. 1941 Jun 15;27(6):254-61
pubmed: 16588454
Dev Comp Immunol. 2015 Sep;52(1):98-106
pubmed: 25956195
Nat Rev Genet. 2018 Apr;19(4):220-234
pubmed: 29335644
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Dev Comp Immunol. 2018 Jan;78:141-148
pubmed: 28966127
Curr Opin Plant Biol. 2020 Apr;54:26-33
pubmed: 31981929
BMC Bioinformatics. 2006 Feb 09;7:62
pubmed: 16469098
G3 (Bethesda). 2020 Apr 9;10(4):1361-1374
pubmed: 32071071
Bioinformatics. 2011 Jun 15;27(12):1691-2
pubmed: 21493652
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
BMC Evol Biol. 2020 May 24;20(1):60
pubmed: 32448128
NAR Genom Bioinform. 2020 Jun;2(2):lqaa026
pubmed: 32440658
J Med Entomol. 2002 Jul;39(4):695-8
pubmed: 12144307
Bioinformatics. 2020 May 1;36(9):2896-2898
pubmed: 31971576
Nature. 2013 Jul 18;499(7458):332-5
pubmed: 23792562
J Insect Sci. 2019 May 1;19(3):
pubmed: 31237955
Genome Biol. 2018 Aug 24;19(1):125
pubmed: 30143029
Curr Opin Genet Dev. 2007 Dec;17(6):513-8
pubmed: 17933508
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Gigascience. 2019 Aug 1;8(8):
pubmed: 31437279
Anim Genet. 2020 Oct;51(5):752-762
pubmed: 32524667
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712