Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
27 Feb 2024
27 Feb 2024
Historique:
received:
02
11
2023
accepted:
14
02
2024
medline:
29
2
2024
pubmed:
28
2
2024
entrez:
27
2
2024
Statut:
epublish
Résumé
Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.
Identifiants
pubmed: 38413611
doi: 10.1038/s41597-024-03077-7
pii: 10.1038/s41597-024-03077-7
pmc: PMC10899175
doi:
Types de publication
Dataset
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
246Informations de copyright
© 2024. The Author(s).
Références
Genomics. 2020 Jan;112(1):581-591
pubmed: 30998967
PLoS One. 2015 Jun 10;10(6):e0117159
pubmed: 26061692
Nat Biotechnol. 2023 May 10;:
pubmed: 37165083
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
Mitochondrial DNA B Resour. 2019 Jul 13;4(2):2533-2534
pubmed: 33365613
Plant Mol Biol. 2011 Jul;76(3-5):273-97
pubmed: 21424877
Bioinformatics. 2020 Apr 1;36(7):2253-2255
pubmed: 31778144
Nucleic Acids Res. 2019 Jul 2;47(W1):W59-W64
pubmed: 30949694
Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Sep;27(5):3668-9
pubmed: 26357910
Sci Data. 2019 Oct 17;6(1):209
pubmed: 31624267
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Front Genet. 2020 Mar 17;11:227
pubmed: 32256523
Sci Rep. 2021 Jan 28;11(1):2506
pubmed: 33510273
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
pubmed: 15215394
Nucleic Acids Res. 2017 Jul 3;45(W1):W6-W11
pubmed: 28486635
Front Plant Sci. 2023 Feb 02;14:1111968
pubmed: 36818825
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302
pubmed: 29029172
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Genome Biol. 2020 Sep 10;21(1):241
pubmed: 32912315
Nat Protoc. 2006;1(5):2320-5
pubmed: 17406474
EMBO J. 1986 Sep;5(9):2043-2049
pubmed: 16453699
Sci Data. 2023 Oct 18;10(1):713
pubmed: 37853021
Mol Biol Evol. 2013 Aug;30(8):1751-60
pubmed: 23676769
Plant Cell. 2021 Aug 31;33(8):2583-2601
pubmed: 34048579
Bioinformatics. 2003;19 Suppl 1:i54-62
pubmed: 12855437
Front Plant Sci. 2022 Feb 10;13:832884
pubmed: 35222490
Nucleic Acids Res. 2017 Feb 28;45(4):e18
pubmed: 28204566
Mol Cells. 2006 Jun 30;21(3):411-7
pubmed: 16819305
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
BMC Genomics. 2021 Feb 4;22(1):103
pubmed: 33541261
Planta Med. 1999 Oct;65(7):658-60
pubmed: 10617409
Genome Biol Evol. 2013;5(5):989-97
pubmed: 23595020
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Nucleic Acids Res. 2004 Jan 02;32(1):11-6
pubmed: 14704338
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
BMC Plant Biol. 2022 May 23;22(1):253
pubmed: 35606691
Curr Protoc Bioinformatics. 2003 Feb;Chapter 10:Unit 10.3
pubmed: 18428693
Mitochondrial DNA B Resour. 2020 Nov 20;5(3):3777-3778
pubmed: 33367099
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604