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Within the family Fabaceae, the genus Glycine is composed of two subgenera annuals (2n=40) and perennials. This life strategy transition may have differentially affected the evolution of various gene families. Its cultivated species G. max has high level of susceptibility to major pathogens including viruses, bacteria and fungi. Understanding nucleotide-binding domain leucine-rich repeat (NLR) genes evolution in soybean is of paramount importance due to their central role in plant immunity and their potential in improving disease resistance in soybean cultivars. In this study, we investigated the significance of this annual-perennial transition on the macroevolution of NLR genes in the genus Glycine. Our results reveal a remarkable distinction between annual species such as Glycine max and Glycine soja, which exhibit an expanded NLRome compared to perennial species (G. cyrtoloba, G. stenophita, G. dolichocarpa, G. falcata, G. syndetika, G. latifolia and G. tomentella). Our evolutionary timescale analysis pinpoints recent accelerated gene duplication events for this expansion, which occurred between 0.1 and 0.5 million years ago, driven predominantly by lineage-specific and terminal duplications. In contrast, perennials initially experienced significant contraction during the diploidisation phase following the Glycine-specific whole-genome duplication event (~10 million years ago). Despite the reduction in the NLRome, perennial lineages exhibit a unique and highly diversified repertoire of NLR genes with limited interspecies synteny. The investigation of gene gain and loss ratios revealed that this diversification resulted from the birth of novel genes following individual speciation events. Among perennials, G. latifolia, a well-known resistance resource, has the highest ratio of these novel genes in the tertiary gene pool. Our study suggests evolutionary mechanisms, including recombination and transposition, as potential drivers for the emergence of these novel genes. This study also provides evidence for the unbalanced expansion of the NLRome in the Dt subgenome compared with the At subgenome in the young allopolyploid G. dolichocarpa. To the best of our knowledge, this is the first study to investigate the effect of annuality and perenniality life transition on the evolution of NLR genes in the genus Glycine to identify its genomics resources for improving the resistance of soybean crop with global importance on the economy and food security.

Abstract Arachis hypogaea is an allotetraploid crop widely grown in the world. Wild relatives of genus Arachis are the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genus Arachis and performed their comparative genomics among four diploids (A. duranensis, A. ipaensis, A. cardenasii, A. stenosperma) and two tetraploid (wild: A. monticola and domesticated: A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified from A. cardenasii, A. stenosperma and A. duranensis, A. hypogaea, A. monticola and A. ipaensis respectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome of A. monticola exhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case of A. hypogaea probably due to distinct natural and artificial selection pressure. In addition, diploid species A. cardenasii revealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure. A. cardenasii and A. monticola can be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genus Arachis to identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security.

Whole genome duplication plays a significant role in plant genome evolution by providing raw materials that can be modified by natural or artificial selection. Nucleotide binding site leucine rich repeat receptor (NLRs) like other gene families are clusters of genes created by duplication and their size reflects the number of duplicated genes. NLR genes encode immune receptors that facilitate identification and binding of effector compounds produced by pathogen as a part of effector triggered immunity (ETI). The accurate identification and characterization of NLR genes substantially contributes to the repertoire of resistance and improves production. The ancestors of Fabaceae family have underwent whole genome duplication (WGD) approximately 58.5 million years ago. In this study, we focused on the subsequent effects of WGD on the evolution of NLR genes within the Vicioid clade, which consists of various legume crops such as chickpea, clover, alfalfa, and pea. The Vicioid clade is divided into three major tribes: Cicereae, Fabeae, and Trifolieae. The analysis of 22 species from the Vicioid clade revealed an overall contraction of the NLRome (the complete set of NLR genes) in members of the Cicereae and Fabeae tribes. This contraction aligns with previous observations that WGD events are often followed by diploidization, leading to a reduced number of duplicated genes. Contrary to this contraction trend, tribe Trifolieae have shown large scale expansion of NLRome irrespective to their genome size. Additionally, the primary diversification of relatively conserved NLR gene subclasses, including helper genes (CCR-NLR) and CCG10-NLR, was reported. Comprehensive evolutionary analysis suggests that NLRome expansion have occurred in during recent 1-6 Mya probably due to their higher substitutions per site per year in Trifolieae. We further hypothesized that this higher rate directed accelerated gene duplications after speciation from their common ancestor and later gene conversion and asymmetric recombination played an active role in subgroup diversification.

Circular single-stranded DNA viruses of the family Geminiviridae encode replication-associated protein (Rep), which is a multifunctional protein involved in virus DNA replication, transcription of virus genes, and suppression of host defense responses. Geminivirus genomes are replicated through the interaction between virus Rep and several host proteins. The Rep also interacts with itself and the virus replication enhancer protein (REn), which is another essential component of the geminivirus replicase complex that interacts with host DNA polymerases α and δ. Recent studies revealed the structural and functional complexities of geminivirus Rep, which is believed to have evolved from plasmids containing a signature domain (HUH) for single-stranded DNA binding with nuclease activity. The Rep coding sequence encompasses the entire coding sequence for AC4, which is intricately embedded within it, and performs several overlapping functions like Rep, supporting virus infection. This review investigated the structural and functional diversity of the geminivirus Rep.

Abstract Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.

Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.