Identification of stress-related genes by co-expression network analysis based on the improved turbot genome.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
29 06 2022
29 06 2022
Historique:
received:
24
02
2022
accepted:
07
06
2022
entrez:
29
6
2022
pubmed:
30
6
2022
medline:
2
7
2022
Statut:
epublish
Résumé
Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.
Identifiants
pubmed: 35768602
doi: 10.1038/s41597-022-01458-4
pii: 10.1038/s41597-022-01458-4
pmc: PMC9243025
doi:
Types de publication
Dataset
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
374Subventions
Organisme : Taishan Scholar Project of Shandong Province
ID : 2019GHY112023
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 31402284
Informations de copyright
© 2022. The Author(s).
Références
Sci Rep. 2017 Aug 21;7(1):8358
pubmed: 28827723
Comp Biochem Physiol Part D Genomics Proteomics. 2020 Mar;33:100632
pubmed: 31715507
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
Biology (Basel). 2020 Aug 13;9(8):
pubmed: 32823553
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Mar Biotechnol (NY). 2021 Aug;23(4):615-627
pubmed: 34426939
Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8708-13
pubmed: 26124135
Genomics. 2021 Jul;113(4):1705-1718
pubmed: 33838278
Int J Parasitol. 2016 Jul;46(8):507-17
pubmed: 27109557
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9
pubmed: 16845043
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10
pubmed: 19274634
Sci Data. 2020 Mar 12;7(1):90
pubmed: 32165614
PLoS One. 2013 Sep 30;8(9):e74682
pubmed: 24098662
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Cancer Lett. 2019 Sep 28;460:29-40
pubmed: 31173855
Methods Mol Biol. 2019;1962:1-14
pubmed: 31020551
J Exp Biol. 2010 Jan 15;213(2):210-24
pubmed: 20038654
Int J Mol Sci. 2018 Feb 08;19(2):
pubmed: 29419805
Immunity. 1998 Jul;9(1):93-103
pubmed: 9697839
Fish Shellfish Immunol. 2019 May;88:65-75
pubmed: 30840856
Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
pubmed: 17130148
PLoS Pathog. 2017 Sep 21;13(9):e1006512
pubmed: 28934357
Blood. 1992 Nov 1;80(9):2363-73
pubmed: 1421407
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Biol Open. 2016 Dec 15;5(12):1784-1789
pubmed: 27793835
Glycobiology. 2007 Aug;17(8):838-46
pubmed: 17483134
BMC Bioinformatics. 2005 Feb 15;6:31
pubmed: 15713233
DNA Res. 2016 Jun;23(3):181-92
pubmed: 26951068
Dev Comp Immunol. 2021 Nov;124:104164
pubmed: 34129850
Nucleic Acids Res. 2013 May 1;41(10):e108
pubmed: 23558742
Ecotoxicol Environ Saf. 2021 Oct 15;223:112613
pubmed: 34388656
Genes (Basel). 2019 Sep 17;10(9):
pubmed: 31533315
Funct Integr Genomics. 2022 Feb;22(1):131-136
pubmed: 34787733
Genome Biol. 2020 Sep 14;21(1):245
pubmed: 32928274
Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
Genome Biol. 2021 Nov 14;22(1):312
pubmed: 34775997
Front Vet Sci. 2020 May 07;7:249
pubmed: 32457922
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654
pubmed: 34320186
Nanomedicine. 2016 Oct;12(7):2007-2017
pubmed: 27288666
Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360
pubmed: 30398656
Animals (Basel). 2021 Apr 30;11(5):
pubmed: 33946507
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Nature. 1973 Nov 16;246(5429):145-6
pubmed: 4148473
BMC Genomics. 2014 Dec 19;15:1149
pubmed: 25526753
J Surg Res. 2015 Mar;194(1):107-13
pubmed: 25450598
Nucleic Acids Res. 2000 Jan 1;28(1):45-8
pubmed: 10592178
J Exp Med. 2005 Feb 21;201(4):509-15
pubmed: 15728234
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Am J Pathol. 2008 Mar;172(3):659-70
pubmed: 18276783
BMC Genomics. 2017 May 6;18(1):352
pubmed: 28477619
Nat Med. 2000 May;6(5):543-8
pubmed: 10802710
J Immunol. 2013 Jun 15;190(12):6360-7
pubmed: 23667110
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
PLoS One. 2012;7(4):e35484
pubmed: 22530030
Plant Physiol. 2018 Mar;176(3):2406-2425
pubmed: 29288233
J Biol Chem. 2011 Jan 21;286(3):1951-8
pubmed: 21098032
Sci Rep. 2021 Jan 15;11(1):1607
pubmed: 33452393
J Mol Biol. 1997 Apr 25;268(1):78-94
pubmed: 9149143
J Therm Biol. 2021 Aug;100:103071
pubmed: 34503808
Proc Natl Acad Sci U S A. 1994 May 10;91(10):4480-4
pubmed: 7514305
Bioinformatics. 2020 May 1;36(9):2896-2898
pubmed: 31971576
Free Radic Biol Med. 2014 Sep;74:274-82
pubmed: 25035076
Int J Mol Sci. 2018 Sep 11;19(9):
pubmed: 30208630
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8
pubmed: 17485477
BMC Biol. 2006 Dec 07;4:41
pubmed: 17156431
BMC Genomics. 2014 Oct 06;15:867
pubmed: 25286752
Bioinformatics. 2019 Jun 1;35(11):1960-1962
pubmed: 30379987
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
Blood. 2005 Apr 15;105(8):3185-92
pubmed: 15632203
Mol Aspects Med. 2020 Dec;76:100887
pubmed: 32838963