Comparative analysis of endogenous plant pararetroviruses in cultivated and wild Dahlia spp.

Abstract

Two distinct caulimoviruses, Dahlia mosaic virus (DMV) and Dahlia common mosaic virus, and an endogenous plant pararetroviral sequence (DvEPRS) were reported in Dahlia spp. DvEPRS, previously referred to as DMV-D10, was originally identified in the US from the cultivated Dahlia variabilis, and has also been found in New Zealand, Lithuania and Egypt, as well as in wild dahlia species growing in their natural habitats in Mexico. Sequence analysis of three new EPRSs from cultivated dahlias from Lithuania [D10-LT; 7,159 nucleotide level (nt)], New Zealand (D10-NZ, 7,156 nt), and the wild species, Dahlia rupicola, from Mexico (D10-DR, 7,133 nt) is reported in this study. The three EPRSs have the structure and organization typical of a caulimovirus species and showed identities among various open reading frames (ORFs) ranging between 71 and 97 % at the nt when compared to those or the known DvEPRS from the US. Examination of a dataset of seven full-length EPRSs obtained to date from cultivated and wild Dahlia spp. provided clues into genetic diversity of these EPRSs from diverse sources of dahlia. Phylogenetic analyses, mutation frequencies, potential recombination events, selection, and fitness were evaluated as evolutionary evidences for genetic variation. Assessment of all ORFs using phylogenomic and population genetics approaches suggests a wide genetic diversity of EPRSs occurring in dahlias. Phylogenetic analyses show that the EPRSs from various sources form one clade indicating a lack of clustering by geographical origin. Grouping of various EPRSs into two host taxa (cultivated vs. wild) shows little divergence with respect to their origin. Population genetic parameters demonstrate negative selection for all ORFs, with the reverse transcriptase region more variable than other ORFs. Recombination events were found which provide evolutionary evidence for genetic diversity among dahlia-associated EPRSs. This study contributes to an increased understanding of molecular population genetics and evolutionary pathways of these reverse transcribing viral elements.

Deep Sequencing Reveals the Complete Genome and Evidence for Transcriptional Activity of the First Virus-Like Sequences Identified in Aristotelia chilensis (Maqui Berry)

“…Conserved characteristic domains between AcV1, Caulimoviridae family virus and Retrotransposon are highlighted. ( A ) Putative domains of AcV1 ORF1 (MP) were aligned with caulimoviruses previously selected by homology searches: CitPRV, PVCV, FMV, Rice tungro bacilliform virus (RTBV) [ 25 ], Dahlia mosaic virus (DMV), DMV-10-NZ, DMV-10-DR [ 26 ], Cauliflower mosaic virus CaMV, and CERV; ( B ) AcV1 ORF2 (RT) were aligned with reverse transcriptases (RT) from Caulimoviruses and a selected retrotransposon. Invariant motifs distinctive of RT’s were underlined and numbered as described by Xiong and Eickbush [ 22 ]; ( C ) AcV1 ORF2 were aligned with Ribonuclease H regions from different Caulimoviruses and Ty3 retrotransposon [ 23 ].…”

“…Phylogenetic analysis is a powerful tool commonly used to make evolutionary comparisons in order to identify relationships between sequences and different species. Aiming to classify the viral family that AcV1 belongs, we built a phylogenetic tree based on the RT protein sequence from AcV1 in comparison with different members of two endogenous Dahlia viruses [ 26 ], CitPRV [ 16 ], one representative member of Florendoviruses based on the Family of different host plants [ 27 ] and Ty3 retrotransposon of S. cerevisiae ( Figure 2 ).…”

Adaptation of pathogens to their local plant host, Silphium integrifolium, along a precipitation gradient

“…Viral sequence was recovered from a S. integrifolium plant with symptoms of Silphium clear vein (SCV) growing in research plantings in Salina, Kansas in 2019 that is similar to the Dahlia common mosaic virus (DCMV) and Dahlia endogenous plant pararetroviral sequence (DvEPRS, formerly DMV-D10; Almeyda et al, 2014), both in the Caulimoviridae family. These sequences have been found in hundreds of other symptomatic S. integrifolium in 2020 (Pappu & Turner, unpublished data).…”

Disease resistance gene count increases with rainfall in Silphium integrifolium

“…Grove (Cybernome; Farr 1989) called leaf blotch hereafter. Recently, Silphium clear vein (SCV) leaf and stem disease has been described and hypothesized to be caused by a virus based on the identification of viral sequences inSilphium integrifolium that are similar to the Dahlia common Mosaic Virus (DCMV) and Dahlia endogenous plant pararetroviral sequence (DvEPRS, formerly DMV-D10) (Almeyda, 2014;Cassetta et al, 2023). Understanding how S. integrifolium defends against these pathogens is crucial for progress in breeding programs and will elucidate evolutionary questions posed in the species (Cassetta et al, 2023, Van Tassel et al, 2017.…”