Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids
<i>Dalbergioid</i> is a large group within the family <i>Fabaceae</i> 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...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/2/377 |
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| author | Shamiza Rani Ramlah Zahra Abu Bakar Muhammad Rizwan Abu-Bakar Sultan Muhammad Zain Amna Mehmood Muhammad Danial Sidra Shakoor Fozia Saleem Ali Serfraz Hafiz Mamoon Rehman Rao Sohail Ahmad Khan Saad Serfraz Saad AlKahtani |
| author_facet | Shamiza Rani Ramlah Zahra Abu Bakar Muhammad Rizwan Abu-Bakar Sultan Muhammad Zain Amna Mehmood Muhammad Danial Sidra Shakoor Fozia Saleem Ali Serfraz Hafiz Mamoon Rehman Rao Sohail Ahmad Khan Saad Serfraz Saad AlKahtani |
| author_sort | Shamiza Rani |
| collection | DOAJ |
| description | <i>Dalbergioid</i> is a large group within the family <i>Fabaceae</i> 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 <i>Dalbergioids</i>. 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 <i>Dalbergioids</i> 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 <i>Dalbergia</i> clade, the expansion of NLRome in six species of the genus <i>Dalbergia</i> was observed, with the exception of <i>Dalbergia odorifera,</i> where a recent contraction of NLRome occurred. Similarly, members of the <i>Pterocarpus</i> clade genus <i>Arachis</i> 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 <i>Arachis</i>. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of <i>Dalbergioids</i> 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 <i>NLR</i> genes in this important tribe. In addition, accurate identification and characterization of <i>NLR</i> genes is a substantial contribution to the repertoire of resistances among members of the <i>Dalbergioids</i> species. |
| first_indexed | 2024-03-11T08:46:42Z |
| format | Article |
| id | doaj.art-34a191a792d64c23892b4af350cd3c84 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T08:46:42Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-34a191a792d64c23892b4af350cd3c842023-11-16T20:42:07ZengMDPI AGGenes2073-44252023-01-0114237710.3390/genes14020377Dynamic Evolution of <i>NLR</i> Genes in DalbergioidsShamiza Rani0Ramlah Zahra1Abu Bakar2Muhammad Rizwan3Abu-Bakar Sultan4Muhammad Zain5Amna Mehmood6Muhammad Danial7Sidra Shakoor8Fozia Saleem9Ali Serfraz10Hafiz Mamoon Rehman11Rao Sohail Ahmad Khan12Saad Serfraz13Saad AlKahtani14Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanMetabolomics Innovative Insitute, University of Alberta, Edmonton, AB T6G 2R3, CanadaEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanCotton Genomics Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanEvolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, PakistanDepartment of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia<i>Dalbergioid</i> is a large group within the family <i>Fabaceae</i> 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 <i>Dalbergioids</i>. 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 <i>Dalbergioids</i> 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 <i>Dalbergia</i> clade, the expansion of NLRome in six species of the genus <i>Dalbergia</i> was observed, with the exception of <i>Dalbergia odorifera,</i> where a recent contraction of NLRome occurred. Similarly, members of the <i>Pterocarpus</i> clade genus <i>Arachis</i> 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 <i>Arachis</i>. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of <i>Dalbergioids</i> 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 <i>NLR</i> genes in this important tribe. In addition, accurate identification and characterization of <i>NLR</i> genes is a substantial contribution to the repertoire of resistances among members of the <i>Dalbergioids</i> species.https://www.mdpi.com/2073-4425/14/2/377<i>NLR</i> geneswild <i>Arachis</i> speciesallotetraploidsallopolyploidNLR expansioncontraction |
| spellingShingle | Shamiza Rani Ramlah Zahra Abu Bakar Muhammad Rizwan Abu-Bakar Sultan Muhammad Zain Amna Mehmood Muhammad Danial Sidra Shakoor Fozia Saleem Ali Serfraz Hafiz Mamoon Rehman Rao Sohail Ahmad Khan Saad Serfraz Saad AlKahtani Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids Genes <i>NLR</i> genes wild <i>Arachis</i> species allotetraploids allopolyploid NLR expansion contraction |
| title | Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids |
| title_full | Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids |
| title_fullStr | Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids |
| title_full_unstemmed | Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids |
| title_short | Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids |
| title_sort | dynamic evolution of i nlr i genes in dalbergioids |
| topic | <i>NLR</i> genes wild <i>Arachis</i> species allotetraploids allopolyploid NLR expansion contraction |
| url | https://www.mdpi.com/2073-4425/14/2/377 |
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