A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).
Beta vulgaris
beet
comparative genomics
genome annotation
genome assembly
Journal
DNA research : an international journal for rapid publication of reports on genes and genomes
ISSN: 1756-1663
Titre abrégé: DNA Res
Pays: England
ID NLM: 9423827
Informations de publication
Date de publication:
01 Feb 2023
01 Feb 2023
Historique:
received:
11
04
2022
revised:
26
08
2022
accepted:
12
09
2022
pubmed:
9
10
2022
medline:
7
2
2023
entrez:
8
10
2022
Statut:
ppublish
Résumé
A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.
Identifiants
pubmed: 36208288
pii: 6748264
doi: 10.1093/dnares/dsac033
pmc: PMC9896481
pii:
doi:
Substances chimiques
Sugars
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : USDA-ARS CRIS
ID : 3635-21000-011-00D
Organisme : Beet Sugar Development Foundation
Organisme : Intramural Research Program of the National Human Genome Research Institute
Organisme : National Institutes of Health
Informations de copyright
Published by Oxford University Press for the Infectious Diseases Society of America 2022.
Références
DNA Res. 2021 Jun 25;28(3):
pubmed: 34254113
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Biochem Genet. 1974 Oct;12(4):257-69
pubmed: 4441361
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Plant Physiol. 2008 Dec;148(4):1772-81
pubmed: 18952863
Plant J. 2017 Feb;89(4):789-804
pubmed: 27862469
Science. 2006 Sep 15;313(5793):1596-604
pubmed: 16973872
Nature. 2017 Feb 16;542(7641):307-312
pubmed: 28178233
Nucleic Acids Res. 2015 Jan;43(Database issue):D1036-41
pubmed: 25428362
Breed Sci. 2019 Jun;69(2):255-265
pubmed: 31481834
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316
Plant J. 2021 Mar;105(6):1495-1506
pubmed: 33300184
Nature. 2007 Sep 27;449(7161):463-7
pubmed: 17721507
Genome Biol. 2013 Jan 30;14(1):R10
pubmed: 23363705
Curr Biol. 2012 Jun 19;22(12):1095-101
pubmed: 22608508
Plant Physiol. 2018 Feb;176(2):1410-1422
pubmed: 29233850
Theor Appl Genet. 2016 Feb;129(2):257-71
pubmed: 26526552
Bioinformatics. 2004 Dec 12;20(18):3643-6
pubmed: 15247098
Mol Plant. 2019 Jun 3;12(6):879-892
pubmed: 30639314
Plant Physiol. 2014 Feb;164(2):513-24
pubmed: 24306534
Plant J. 2018 May 23;:
pubmed: 29797366
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
G3 (Bethesda). 2019 May 7;9(5):1331-1337
pubmed: 30923135
PLoS One. 2016 May 05;11(5):e0152706
pubmed: 27148975
Nat Methods. 2011 Sep 29;8(10):785-6
pubmed: 21959131
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
J Hist Biol. 1998 Summer;31(2):241-62
pubmed: 11620305
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25
pubmed: 14534192
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
BMC Genomics. 2020 Mar 2;21(1):189
pubmed: 32122300
Mol Gen Genet. 1991 Mar;225(3):453-8
pubmed: 1673221
Plant J. 2019 Sep;99(6):1242-1253
pubmed: 31104348
Nature. 2014 Jan 23;505(7484):546-9
pubmed: 24352233
Theor Appl Genet. 1991 Oct;82(6):793-9
pubmed: 24213457
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
BMC Plant Biol. 2016 May 26;16(1):120
pubmed: 27230558
Theor Appl Genet. 2017 Sep;130(9):1857-1866
pubmed: 28589246
Science. 2010 Dec 3;330(6009):1397-400
pubmed: 21127254
Trends Plant Sci. 2019 Aug;24(8):700-724
pubmed: 31208890
Mol Biol Evol. 2015 Aug;32(8):2001-14
pubmed: 25837578
Plant Cell. 2005 Nov;17(11):3007-18
pubmed: 16227453
Plant J. 2012 May;70(3):528-40
pubmed: 22211633
Cytometry A. 2003 Feb;51(2):127-8; author reply 129
pubmed: 12541287
J Mol Biol. 2001 Jan 19;305(3):567-80
pubmed: 11152613
Physiol Plant. 2009 Jan;135(1):84-97
pubmed: 19121102
Annu Rev Plant Biol. 2014;65:505-30
pubmed: 24579996
BMC Biol. 2017 Aug 31;15(1):74
pubmed: 28854926
Plant J. 2012 Nov;72(4):600-11
pubmed: 22775355
Nat Genet. 2012 Jun 03;44(7):816-20
pubmed: 22660548
PLoS Comput Biol. 2020 Jun 26;16(6):e1007981
pubmed: 32589667
Plant Sci. 2013 Jun;207:72-8
pubmed: 23602101
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Genome Res. 2016 Mar;26(3):342-50
pubmed: 26848124
Nat Genet. 2015 Jan;47(1):92-6
pubmed: 25436858
Chromosome Res. 2006;14(8):881-97
pubmed: 17195925
BMC Bioinformatics. 2004 May 14;5:59
pubmed: 15144565
Plant Cell. 2002 Sep;14(9):2015-29
pubmed: 12215502