Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.
Bombus
gene family evolution
genome assembly
genome evolution
insect diversity
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
23 01 2021
23 01 2021
Historique:
pubmed:
19
9
2020
medline:
22
6
2021
entrez:
18
9
2020
Statut:
ppublish
Résumé
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.
Identifiants
pubmed: 32946576
pii: 5908523
doi: 10.1093/molbev/msaa240
pmc: PMC7826183
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
486-501Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG004037
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010485
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : ErratumIn
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Annu Rev Entomol. 2008;53:191-208
pubmed: 17803456
Syst Biol. 2007 Feb;56(1):17-24
pubmed: 17366134
Trends Ecol Evol. 1987 Sep;2(9):272-5
pubmed: 21227865
Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11857-11865
pubmed: 31043564
PLoS Biol. 2016 Oct 4;14(10):e1002564
pubmed: 27701411
Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4656-60
pubmed: 23487768
BMC Genomics. 2016 Mar 05;17:187
pubmed: 26944054
J Neurochem. 2006 May;97(3):872-83
pubmed: 16573648
Conserv Biol. 2009 Aug;23(4):931-40
pubmed: 19245487
Bioinformatics. 2008 Jul 1;24(13):1538-9
pubmed: 18474506
Mol Ecol. 2019 Feb;28(4):746-760
pubmed: 30576015
Annu Rev Entomol. 2002;47:93-122
pubmed: 11729070
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
PLoS Biol. 2020 Dec 3;18(12):e3000954
pubmed: 33270638
Genome Res. 2010 Aug;20(8):1084-96
pubmed: 20601587
Mol Biol Evol. 2019 Jun 1;36(6):1215-1219
pubmed: 30865278
BMC Bioinformatics. 2014 Aug 15;15:281
pubmed: 25128196
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
BMC Evol Biol. 2019 Jan 29;19(1):36
pubmed: 30696414
Arch Insect Biochem Physiol. 2001 Jun;47(2):86-99
pubmed: 11376455
Nature. 2008 Jul 24;454(7203):519-22
pubmed: 18594516
Science. 2015 Mar 27;347(6229):1255957
pubmed: 25721506
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):662-7
pubmed: 21199943
Mol Ecol. 2019 Mar;28(6):1537-1549
pubmed: 30003608
Insect Biochem Mol Biol. 2017 Apr;83:21-34
pubmed: 28232040
Nat Commun. 2019 Dec 20;10(1):5818
pubmed: 31862875
PLoS Biol. 2016 Feb 12;14(2):e1002379
pubmed: 26871574
Zootaxa. 2016 Dec 01;4204(1):zootaxa.4204.1.1
pubmed: 27988613
Zootaxa. 2019 Jul 03;4625(1):zootaxa.4625.1.1
pubmed: 31712545
Mol Ecol. 2020 Mar;29(5):920-939
pubmed: 32031739
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
pubmed: 15961478
Bioinformatics. 2011 Jul 1;27(13):i275-82
pubmed: 21685081
Genome Biol. 2020 Jan 23;21(1):15
pubmed: 31969194
Oecologia. 2013 Dec;173(4):1649-60
pubmed: 23852029
Syst Biol. 2018 Jan 01;67(1):158-169
pubmed: 28973673
Nucleic Acids Res. 2015 Jan;43(Database issue):D250-6
pubmed: 25428351
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Am J Hum Genet. 2016 Dec 1;99(6):1338-1352
pubmed: 27839872
Annu Rev Entomol. 2001;46:31-78
pubmed: 11112163
Mol Ecol. 2013 Mar;22(6):1503-17
pubmed: 23293987
Proc Biol Sci. 2017 May 17;284(1854):
pubmed: 28469019
Nature. 2006 Oct 26;443(7114):931-49
pubmed: 17073008
EBioMedicine. 2019 Feb;40:717-732
pubmed: 30713114
Genome Res. 2008 Jan;18(1):188-96
pubmed: 18025269
Nucleic Acids Res. 2019 Jan 25;47(2):594-606
pubmed: 30535227
Curr Biol. 2019 Jan 21;29(2):283-293.e5
pubmed: 30612904
Methods. 2012 Nov;58(3):268-76
pubmed: 22652625
Proc Biol Sci. 2017 Jul 26;284(1859):
pubmed: 28724728
PLoS One. 2012;7(8):e43111
pubmed: 22912801
Heredity (Edinb). 2007 Apr;98(4):189-97
pubmed: 17389895
BMC Genomics. 2015 Jan 02;16:1
pubmed: 25553907
Syst Biol. 2008 Feb;57(1):58-75
pubmed: 18275002
BMC Bioinformatics. 2008 Jan 14;9:18
pubmed: 18194517
Science. 2014 Dec 12;346(6215):1320-31
pubmed: 25504713
Mol Biol Evol. 2015 May;32(5):1342-53
pubmed: 25697341
Mol Biol Evol. 2015 Mar;32(3):820-32
pubmed: 25540451
Nature. 2007 Nov 8;450(7167):203-18
pubmed: 17994087
Nucleic Acids Res. 2009 Nov;37(21):e143
pubmed: 19762481
Trends Ecol Evol. 2010 Jun;25(6):345-53
pubmed: 20188434
Nat Genet. 2018 May;50(5):754-763
pubmed: 29700467
Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4386-91
pubmed: 27044096
Elife. 2013 Dec 03;2:e01179
pubmed: 24302569
Science. 2013 Mar 29;339(6127):1608-11
pubmed: 23449997
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Genome Biol. 2015 Apr 24;16:76
pubmed: 25908251
Biodivers Data J. 2015 Dec 30;(3):e6833
pubmed: 26751762
PLoS Genet. 2012;8(7):e1002764
pubmed: 22807683
Front Genet. 2015 Apr 10;6:124
pubmed: 25914717
Science. 2015 Jul 10;349(6244):177-80
pubmed: 26160945
Annu Rev Entomol. 2020 Jan 7;65:209-232
pubmed: 31610137
Science. 2020 Feb 7;367(6478):685-688
pubmed: 32029628
Mol Biol Evol. 2016 Dec;33(12):3108-3132
pubmed: 27604222
Mech Dev. 2001 Jun;104(1-2):79-87
pubmed: 11404082
J Exp Biol. 2015 Jul;218(Pt 14):2233-40
pubmed: 26202778
BMC Genomics. 2011 Dec 20;12:623
pubmed: 22185240
Annu Rev Genet. 2013;47:121-37
pubmed: 23988117
Mol Biol Evol. 2013 Aug;30(8):1987-97
pubmed: 23709260
Mol Biol Evol. 2020 Sep 1;37(9):2727-2733
pubmed: 32365179
J Exp Biol. 2003 Dec;206(Pt 24):4393-412
pubmed: 14610026
Genome Res. 2011 Sep;21(9):1512-28
pubmed: 21665927
BMC Evol Biol. 2007 Nov 15;7:226
pubmed: 18005411
PLoS Biol. 2006 Jan;4(1):e1
pubmed: 16332160
Genome Biol Evol. 2020 Jan 1;12(1):3677-3683
pubmed: 31860080
Genome Res. 2011 Dec;21(12):2096-113
pubmed: 21994247
Syst Biol. 2016 Jul;65(4):711-21
pubmed: 26927960
Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6535-42
pubmed: 15851677
Genome Biol. 2015 Apr 24;16:83
pubmed: 25908406
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
J Clin Biochem Nutr. 2011 Jan;48(1):20-5
pubmed: 21297907
Agric Ecosyst Environ. 2019 Sep 1;281:124-133
pubmed: 31481820
Annu Rev Entomol. 2014;59:299-319
pubmed: 24160431
Science. 2015 Jan 2;347(6217):1258522
pubmed: 25554792
BMC Bioinformatics. 2018 May 8;19(Suppl 6):153
pubmed: 29745866
Annu Rev Entomol. 2016;61:177-96
pubmed: 26982439
J Insect Physiol. 2019 Aug - Sep;117:103894
pubmed: 31175854
Science. 2020 May 22;368(6493):881-884
pubmed: 32439792