Dynamic Evolution of NLR Genes in Dalbergioids

Author:

Rani Shamiza1ORCID,Zahra Ramlah1,Bakar Abu1,Rizwan Muhammad1ORCID,Sultan Abu-Bakar1,Zain Muhammad1,Mehmood Amna1,Danial Muhammad1,Shakoor Sidra1,Saleem Fozia2,Serfraz Ali13,Rehman Hafiz Mamoon1,Khan Rao Sohail Ahmad4,Serfraz Saad1ORCID,AlKahtani Saad5ORCID

Affiliation:

1. Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan

2. Metabolomics Innovative Insitute, University of Alberta, Edmonton, AB T6G 2R3, Canada

3. Department of Plant Pathology, University of Arid Agriculture, Rawalpindi 46000, Pakistan

4. Cotton Genomics Lab, Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan

5. Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia

Abstract

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.

Funder

King Saud University

Publisher

MDPI AG

Subject

Genetics (clinical),Genetics

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