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Dynamic Evolution of NLR Genes in Dalbergioids

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. Th...

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Autores principales: Rani, Shamiza, Zahra, Ramlah, Bakar, Abu, Rizwan, Muhammad, Sultan, Abu-Bakar, Zain, Muhammad, Mehmood, Amna, Danial, Muhammad, Shakoor, Sidra, Saleem, Fozia, Serfraz, Ali, Rehman, Hafiz Mamoon, Khan, Rao Sohail Ahmad, Serfraz, Saad, AlKahtani, Saad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9956324/
https://www.ncbi.nlm.nih.gov/pubmed/36833304
http://dx.doi.org/10.3390/genes14020377
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author Rani, Shamiza
Zahra, Ramlah
Bakar, Abu
Rizwan, Muhammad
Sultan, Abu-Bakar
Zain, Muhammad
Mehmood, Amna
Danial, Muhammad
Shakoor, Sidra
Saleem, Fozia
Serfraz, Ali
Rehman, Hafiz Mamoon
Khan, Rao Sohail Ahmad
Serfraz, Saad
AlKahtani, Saad
author_facet Rani, Shamiza
Zahra, Ramlah
Bakar, Abu
Rizwan, Muhammad
Sultan, Abu-Bakar
Zain, Muhammad
Mehmood, Amna
Danial, Muhammad
Shakoor, Sidra
Saleem, Fozia
Serfraz, Ali
Rehman, Hafiz Mamoon
Khan, Rao Sohail Ahmad
Serfraz, Saad
AlKahtani, Saad
author_sort Rani, Shamiza
collection PubMed
description Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species.
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spelling pubmed-99563242023-02-25 Dynamic Evolution of NLR Genes in Dalbergioids Rani, Shamiza Zahra, Ramlah Bakar, Abu Rizwan, Muhammad Sultan, Abu-Bakar Zain, Muhammad Mehmood, Amna Danial, Muhammad Shakoor, Sidra Saleem, Fozia Serfraz, Ali Rehman, Hafiz Mamoon Khan, Rao Sohail Ahmad Serfraz, Saad AlKahtani, Saad Genes (Basel) Article Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species. MDPI 2023-01-31 /pmc/articles/PMC9956324/ /pubmed/36833304 http://dx.doi.org/10.3390/genes14020377 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rani, Shamiza
Zahra, Ramlah
Bakar, Abu
Rizwan, Muhammad
Sultan, Abu-Bakar
Zain, Muhammad
Mehmood, Amna
Danial, Muhammad
Shakoor, Sidra
Saleem, Fozia
Serfraz, Ali
Rehman, Hafiz Mamoon
Khan, Rao Sohail Ahmad
Serfraz, Saad
AlKahtani, Saad
Dynamic Evolution of NLR Genes in Dalbergioids
title Dynamic Evolution of NLR Genes in Dalbergioids
title_full Dynamic Evolution of NLR Genes in Dalbergioids
title_fullStr Dynamic Evolution of NLR Genes in Dalbergioids
title_full_unstemmed Dynamic Evolution of NLR Genes in Dalbergioids
title_short Dynamic Evolution of NLR Genes in Dalbergioids
title_sort dynamic evolution of nlr genes in dalbergioids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9956324/
https://www.ncbi.nlm.nih.gov/pubmed/36833304
http://dx.doi.org/10.3390/genes14020377
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