A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici.
Manual curation
TE consensus
TE library
Transposable Elements
Transposons
Zymoseptoria tritici
Journal
BMC research notes
ISSN: 1756-0500
Titre abrégé: BMC Res Notes
Pays: England
ID NLM: 101462768
Informations de publication
Date de publication:
16 Nov 2023
16 Nov 2023
Historique:
received:
29
09
2023
accepted:
03
11
2023
medline:
27
11
2023
pubmed:
17
11
2023
entrez:
17
11
2023
Statut:
epublish
Résumé
High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs. A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom. Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.
Identifiants
pubmed: 37974222
doi: 10.1186/s13104-023-06613-7
pii: 10.1186/s13104-023-06613-7
pmc: PMC10652580
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
335Subventions
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung,Switzerland
ID : 201149
Informations de copyright
© 2023. The Author(s).
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9
pubmed: 26612867
Nat Commun. 2023 Feb 24;14(1):1059
pubmed: 36828814
Curr Opin Genet Dev. 2016 Apr;37:90-100
pubmed: 26855260
BMC Genomics. 2020 Aug 26;21(1):588
pubmed: 32842972
Microb Genom. 2021 Oct;7(10):
pubmed: 34617882
PLoS Genet. 2011 Jun;7(6):e1002070
pubmed: 21695235
Nat Rev Genet. 2007 Dec;8(12):973-82
pubmed: 17984973
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Mob DNA. 2022 Feb 16;13(1):5
pubmed: 35172896
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
BMC Biol. 2018 Jan 11;16(1):5
pubmed: 29325559
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Plant Mol Biol. 2000 Jan;42(1):251-69
pubmed: 10688140
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
BMC Biol. 2020 Feb 11;18(1):12
pubmed: 32046716
Mob DNA. 2021 Jan 12;12(1):2
pubmed: 33436076
DNA Res. 2012;19(1):11-21
pubmed: 22086996
Bioinformatics. 2013 Oct 1;29(19):2487-9
pubmed: 23842809
J Mol Biol. 2000 Sep 8;302(1):205-17
pubmed: 10964570
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Annu Rev Genet. 2007;41:331-68
pubmed: 18076328
Mob DNA. 2022 Mar 30;13(1):7
pubmed: 35354491