Almeyda C V, Eid S G, Saar D, Samuitiene M, Pappu H R
Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
Virus Genes. 2014 Feb;48(1):140-52. doi: 10.1007/s11262-013-0997-9. Epub 2013 Dec 19.
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.
在大丽花属植物中发现了两种不同的花椰菜花叶病毒，即大丽花花叶病毒（DMV）和大丽花普通花叶病毒，以及一种内源性植物类逆转录病毒序列（DvEPRS）。DvEPRS，以前称为DMV-D10，最初在美国从栽培的大丽花中鉴定出来，在新西兰、立陶宛和埃及也有发现，在墨西哥自然栖息地生长的野生大丽花物种中也有发现。本研究报道了来自立陶宛栽培大丽花（D10-LT；7159个核苷酸水平（nt））、新西兰（D10-NZ，7156 nt）和墨西哥野生物种大丽花（D10-DR，7133 nt）的三个新EPRSs的序列分析。这三个EPRSs具有花椰菜花叶病毒物种典型的结构和组织，与来自美国的已知DvEPRS相比，在核苷酸水平上，各种开放阅读框（ORF）之间的同一性在71%至97%之间。对迄今为止从栽培和野生大丽花属植物中获得的七个全长EPRSs数据集的研究为这些来自不同大丽花来源的EPRSs的遗传多样性提供了线索。系统发育分析、突变频率、潜在重组事件、选择和适应性被评估为遗传变异的进化证据。使用系统基因组学和群体遗传学方法对所有ORF进行评估表明，大丽花中存在的EPRSs具有广泛的遗传多样性。系统发育分析表明，来自不同来源的EPRSs形成一个分支，表明缺乏按地理起源的聚类。将各种EPRSs分为两个宿主类群（栽培与野生）显示出它们的起源差异很小。群体遗传参数表明所有ORF都受到负选择，逆转录酶区域比其他ORF更具变异性。发现了重组事件，为与大丽花相关的EPRSs之间的遗传多样性提供了进化证据。本研究有助于增进对这些逆转录病毒元件的分子群体遗传学和进化途径的理解。
