De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome.
Bruguiera sexangula
10×
Genomics
genome assembly
mangrove
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
04 02 2022
04 02 2022
Historique:
accepted:
01
02
2022
pubmed:
12
2
2022
medline:
1
4
2022
entrez:
11
2
2022
Statut:
ppublish
Résumé
Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10× Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bases. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves' physiological and morphological adaptations to the intertidal zones.
Identifiants
pubmed: 35148390
pii: 6527208
doi: 10.1093/gbe/evac025
pmc: PMC8872974
pii:
doi:
Banques de données
figshare
['10.6084/m9.figshare.16625905.v1']
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) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Ann Bot. 2005 Jan;95(1):99-110
pubmed: 15596459
Genomics. 1997 Nov 15;46(1):37-45
pubmed: 9403056
Mol Ecol Resour. 2021 Jan;21(1):238-250
pubmed: 32794377
Mol Ecol Resour. 2021 Jan;21(1):212-225
pubmed: 32841550
Bioinformatics. 2006 Nov 1;22(21):2688-90
pubmed: 16928733
Ann Bot. 2007 Oct;100(4):875-88
pubmed: 17684025
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Genome Biol. 2019 Oct 28;20(1):224
pubmed: 31661016
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
G3 (Bethesda). 2022 Feb 02;:
pubmed: 35106563
Sci Rep. 2018 Sep 5;8(1):13298
pubmed: 30185918
Gigascience. 2019 Mar 1;8(3):
pubmed: 30624602
BMC Genomics. 2009 Jan 09;10:14
pubmed: 19134208
Nucleic Acids Res. 2012 Apr;40(7):e49
pubmed: 22217600
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Methods Mol Biol. 2019;1962:65-95
pubmed: 31020555
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17519-24
pubmed: 23045684
Nature. 2001 Feb 22;409(6823):1092-101
pubmed: 11234023
Sci Rep. 2017 Aug 30;7(1):10031
pubmed: 28855698
Genomics. 2021 Jul;113(4):2221-2228
pubmed: 34022344
Nucleic Acids Res. 2015 Jan;43(Database issue):D250-6
pubmed: 25428351
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
BMC Genomics. 2015 Aug 14;16:605
pubmed: 26272068
Natl Sci Rev. 2017 Sep;4(5):721-734
pubmed: 31258950
G3 (Bethesda). 2021 Jan 18;11(1):
pubmed: 33561229
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
New Phytol. 2021 Sep;231(6):2346-2358
pubmed: 34115401
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Bioinformatics. 2005 May 1;21(9):1859-75
pubmed: 15728110
Hortic Res. 2020 May 2;7(1):75
pubmed: 32377365
Mol Ecol Resour. 2022 Jan 21;:
pubmed: 35060320
Biosci Biotechnol Biochem. 2009 Feb;73(2):304-10
pubmed: 19202291
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12
pubmed: 15215400
Am Nat. 2005 Mar;165(3):E36-65
pubmed: 15729659
Mar Genomics. 2015 Oct;23:33-6
pubmed: 25899405