Investigation of NLR Genes Reveals Divergent Evolution on NLRome in Diploid and Polyploid Species in Genus Trifolium

Abstract

Crop wild relatives contain a greater variety of phenotypic and genotypic diversity compared to their domesticated counterparts. Trifolium crop species have limited genetic diversity to cope with biotic and abiotic stresses due to artificial selection for consumer preferences. Here, we investigated the distribution and evolution of nucleotide-binding site leucine-rich repeat receptor (NLR) genes in the genus of Trifolium with the objective to identify reference NLR genes. We identified 412, 350, 306, 389 and 241 NLR genes were identified from Trifolium. subterraneum, T. pratense, T. occidentale, subgenome-A of T. repens and subgenome-B of T. repens, respectively. Phylogenetic and clustering analysis reveals seven sub-groups in genus Trifolium. Specific subgroups such as G4-CNL, CCG10-CNL and TIR-CNL show distinct duplication patterns in specific species, which suggests subgroup duplications that are the hallmarks of their divergent evolution. Furthermore, our results strongly suggest the overall expansion of NLR repertoire in T. subterraneum is due to gene duplication events and birth of gene families after speciation. Moreover, the NLRome of the allopolyploid species T. repens has evolved asymmetrically, with the subgenome -A showing expansion, while the subgenome-B underwent contraction. These findings provide crucial background data for comprehending NLR evolution in the Fabaceae family and offer a more comprehensive analysis of NLR genes as disease resistance genes.

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

“…Duplication and polyploidization are significant contributors to plant speciation and divergence as they result in the creation of novel gene functions, and neo-functionalization of duplicated genes as well as recombination [66]. Furthermore, transpositions and structural variation might also play a role in the divergent evolution of genes [67]. Genome-wide studies of various gene families in Brassicaceae have consistently indicated their expansion compared with Arabidopsis.…”

Investigation of Resistance Genes in Genus Vigna Reveals Highly Variable NLRome in Parallel Domesticated Member Species

“…Extinction of pathogen often lead to death of several NLR genes to maintain host fitness [ 33 ]. Among Fabaceae family, several members have been investigated including Dalbergioids , genus Cicer and genus Trifolium [ 22 , 32 , 37 ]. One common observation, was the importance of crop wild relatives (CWRs) that contain broader and expanded NLRome and conversely domesticated crop species suffers from narrowing of genetic diversity [ 22 , 32 , 37 ].…”

“…Among Fabaceae family, several members have been investigated including Dalbergioids , genus Cicer and genus Trifolium [ 22 , 32 , 37 ]. One common observation, was the importance of crop wild relatives (CWRs) that contain broader and expanded NLRome and conversely domesticated crop species suffers from narrowing of genetic diversity [ 22 , 32 , 37 ]. Secondly, presence of polyploidy have considerably broaden and expanded the NLRome of allotetraploid species of Arachis and Trifolium [ 22 , 32 ].…”

“…One common observation, was the importance of crop wild relatives (CWRs) that contain broader and expanded NLRome and conversely domesticated crop species suffers from narrowing of genetic diversity [ 22 , 32 , 37 ]. Secondly, presence of polyploidy have considerably broaden and expanded the NLRome of allotetraploid species of Arachis and Trifolium [ 22 , 32 ]. However, genus Vigna only contain one polyploid species among 104 member species, yet its members contain highly diversified repertoire of NLR genes.…”

“…Secondly, we further screened basal expression levels of NLR genes in V. unguiculata , where in total 28 sample were used to compared the expression between different tissues. We utilized the HISAT, Stringtie and Ballgown based alignment and quantification pipeline as already mentioned in previous article [ 22 , 32 ].…”