De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum.
Chrysanthemum makinoi
annotation
chrysanthemum
genome assembly
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
04 01 2022
04 01 2022
Historique:
received:
09
07
2021
accepted:
23
09
2021
pubmed:
2
12
2021
medline:
9
3
2022
entrez:
1
12
2021
Statut:
ppublish
Résumé
Chrysanthemum is among the top 10 cut, potted, and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here, we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The cultivated hexaploid varieties are thought to originate from a hybrid of wild chrysanthemums, among which the diploid Chrysanthemum makinoi has been mentioned. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences, and a genetic map, we assembled 3.1 Gb of its sequence into nine pseudochromosomes, with an N50 of 330 Mb and a BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95,074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution, and history.
Identifiants
pubmed: 34849775
pii: 6395362
doi: 10.1093/g3journal/jkab358
pmc: PMC8727959
pii:
doi:
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) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
Références
Nucleic Acids Res. 2018 Nov 30;46(21):e126
pubmed: 30107434
Theor Appl Genet. 2010 Feb;120(3):491-508
pubmed: 19826774
Mol Plant. 2018 Dec 3;11(12):1482-1491
pubmed: 30342096
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Science. 2009 Nov 20;326(5956):1112-5
pubmed: 19965430
Mitochondrial DNA B Resour. 2018 Apr 28;3(2):549-550
pubmed: 33474235
Genome Res. 2016 Dec;26(12):1721-1729
pubmed: 27852649
Nat Biotechnol. 2015 May;33(5):524-30
pubmed: 25893780
Nucleic Acids Res. 2000 Jan 1;28(1):45-8
pubmed: 10592178
Plant Sci. 2019 Oct;287:110174
pubmed: 31481216
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Bioinformatics. 2019 Nov 1;35(21):4430-4432
pubmed: 31095290
Genome Biol. 2015 Jan 13;16:3
pubmed: 25583564
Sci Rep. 2016 Jan 20;6:19427
pubmed: 26786968
Mol Plant. 2018 Jun 4;11(6):776-788
pubmed: 29703587
Chromosome Res. 2011 Oct;19(7):939-53
pubmed: 21987187
Plant Mol Biol. 2017 Nov;95(4-5):451-461
pubmed: 29052098
Nat Genet. 2019 Mar;51(3):541-547
pubmed: 30804557
DNA Res. 2019 Jun 1;26(3):195-203
pubmed: 30689773
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Mitochondrial DNA B Resour. 2018 Apr 27;3(2):529-530
pubmed: 33474229
Theor Appl Genet. 2011 Sep;123(5):779-91
pubmed: 21647740
Bioinformatics. 2016 Jan 15;32(2):292-4
pubmed: 26428292
Nucleic Acids Res. 2008 Jun;36(10):3420-35
pubmed: 18445632
Nature. 2017 Jun 1;546(7656):148-152
pubmed: 28538728
Sci Rep. 2014 Oct 23;4:6730
pubmed: 25339092
Science. 2014 Jul 18;345(6194):1251788
pubmed: 25035500
Annu Rev Plant Biol. 2007;58:377-406
pubmed: 17280525
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595
pubmed: 28594827
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Plant Physiol. 2014 Nov;166(3):1241-54
pubmed: 25209985
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
BMC Bioinformatics. 2018 Nov 29;19(1):460
pubmed: 30497373
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457
pubmed: 32300014
Theor Appl Genet. 2017 Dec;130(12):2527-2541
pubmed: 28852802
Nat Genet. 2016 Apr;48(4):438-46
pubmed: 26901068
G3 (Bethesda). 2020 Sep 2;10(9):3047-3060
pubmed: 32601059
PLoS One. 2012;7(11):e48970
pubmed: 23133665
Theor Appl Genet. 1986 Jun;72(3):314-21
pubmed: 24247937
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Cytometry A. 2011 Jun;79(6):401-4
pubmed: 21472847
Trends Genet. 2018 Sep;34(9):666-681
pubmed: 29941292
Chromosome Res. 2018 Mar;26(1-2):5-23
pubmed: 29332159
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Front Plant Sci. 2018 Nov 21;9:1660
pubmed: 30519250
Plant Cell. 2014 Jul;26(7):2761-76
pubmed: 24989045
Int J Mol Sci. 2016 Nov 28;17(12):
pubmed: 27916797
BMC Genomics. 2017 Aug 7;18(1):585
pubmed: 28784083
Genomics Proteomics Bioinformatics. 2016 Dec;14(6):357-370
pubmed: 27998811
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
BMC Genomics. 2013 Oct 06;14:686
pubmed: 24093210
Nat Commun. 2020 Jan 17;11(1):340
pubmed: 31953413