Cargando…

Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica

Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which i...

Descripción completa

Detalles Bibliográficos
Autores principales: Tong, Chunyan, Zhang, Yutong, Shi, Fengling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9871256/
https://www.ncbi.nlm.nih.gov/pubmed/36704335
http://dx.doi.org/10.3389/fgene.2022.1088763
_version_ 1784877128382152704
author Tong, Chunyan
Zhang, Yutong
Shi, Fengling
author_facet Tong, Chunyan
Zhang, Yutong
Shi, Fengling
author_sort Tong, Chunyan
collection PubMed
description Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which is the largest family of plant disease resistance genes (R genes). A total of 338 NLR genes were identified in the M. ruthenica genome, including 160 typical genes that contained 80 coiled-coil (CC)-NBS-LRR (CNL) genes, 76 toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes, four resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) subclass genes, and 178 atypical NLR genes encoding proteins without at least one important domain. Among its eight chromosomes, M. ruthenica chromosomes 3 and 8 contained most of the NLR genes. More than 40% of all NLR genes were located on these two chromosomes, mainly in multigene clusters. The NLR proteins of M. ruthenica had six highly conserved motifs: P-loop, GLPL, RNBS-D, kinase-2, RNBS-C, and MHDV. Phylogenetic analysis revealed that the NLR genes of M. ruthenica formed three deeply separated clades according to the N-terminal domain of the proteins encoded by these genes. Gene duplication and syntenic analysis suggested four gene duplication types in the NLR genes of M. ruthenica, namely, tandem, proximal, dispersed, and segmental duplicates, which involved 189, 49, 59, and 41 genes, respectively. A total of 41 segmental duplication genes formed 23 NLR gene pairs located on syntenic chromosomal blocks mainly between chromosomes 6 and 7. In addition, syntenic analysis between M. truncatula and M. ruthenica revealed 193 gene pairs located on syntenic chromosomal blocks of the two species. The expression analysis of M. ruthenica NLR genes showed that 303 (89.6%) of the NLR genes were expressed in different varieties. Overall, this study described the full NLR profile of the M. ruthenica genome to provide an important resource for mining disease-resistant genes and disease-resistant breeding.
format Online
Article
Text
id pubmed-9871256
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-98712562023-01-25 Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica Tong, Chunyan Zhang, Yutong Shi, Fengling Front Genet Genetics Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which is the largest family of plant disease resistance genes (R genes). A total of 338 NLR genes were identified in the M. ruthenica genome, including 160 typical genes that contained 80 coiled-coil (CC)-NBS-LRR (CNL) genes, 76 toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes, four resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) subclass genes, and 178 atypical NLR genes encoding proteins without at least one important domain. Among its eight chromosomes, M. ruthenica chromosomes 3 and 8 contained most of the NLR genes. More than 40% of all NLR genes were located on these two chromosomes, mainly in multigene clusters. The NLR proteins of M. ruthenica had six highly conserved motifs: P-loop, GLPL, RNBS-D, kinase-2, RNBS-C, and MHDV. Phylogenetic analysis revealed that the NLR genes of M. ruthenica formed three deeply separated clades according to the N-terminal domain of the proteins encoded by these genes. Gene duplication and syntenic analysis suggested four gene duplication types in the NLR genes of M. ruthenica, namely, tandem, proximal, dispersed, and segmental duplicates, which involved 189, 49, 59, and 41 genes, respectively. A total of 41 segmental duplication genes formed 23 NLR gene pairs located on syntenic chromosomal blocks mainly between chromosomes 6 and 7. In addition, syntenic analysis between M. truncatula and M. ruthenica revealed 193 gene pairs located on syntenic chromosomal blocks of the two species. The expression analysis of M. ruthenica NLR genes showed that 303 (89.6%) of the NLR genes were expressed in different varieties. Overall, this study described the full NLR profile of the M. ruthenica genome to provide an important resource for mining disease-resistant genes and disease-resistant breeding. Frontiers Media S.A. 2023-01-10 /pmc/articles/PMC9871256/ /pubmed/36704335 http://dx.doi.org/10.3389/fgene.2022.1088763 Text en Copyright © 2023 Tong, Zhang and Shi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Tong, Chunyan
Zhang, Yutong
Shi, Fengling
Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title_full Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title_fullStr Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title_full_unstemmed Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title_short Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica
title_sort genome-wide identification and analysis of the nlr gene family in medicago ruthenica
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9871256/
https://www.ncbi.nlm.nih.gov/pubmed/36704335
http://dx.doi.org/10.3389/fgene.2022.1088763
work_keys_str_mv AT tongchunyan genomewideidentificationandanalysisofthenlrgenefamilyinmedicagoruthenica
AT zhangyutong genomewideidentificationandanalysisofthenlrgenefamilyinmedicagoruthenica
AT shifengling genomewideidentificationandanalysisofthenlrgenefamilyinmedicagoruthenica