Abstract Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5′ terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3′ terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.

中文翻译：

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马铃薯Y病毒及其坏死重组体全球群体的系统发育


摘要 马铃薯Y病毒（PVY）是全世界马铃薯和其他茄科作物的主要病原体。它与首先或仅在美洲发现的马铃薯病毒组关系最为密切，几乎可以肯定它起源于安第斯山脉，其宿主在那里被驯化。我们推断了自 1938 年以来在全世界收集的 240 个 PVY 分离株（但不是安第斯山脉）已发表的基因组序列的系统发育。所有这些都分为五个分组，它们大部分（但不完全）与已经使用生物和分类数据设计的分组相对应。只有 42% 的序列不是重组的，所有这些序列都属于三个系统群中的一个或另一个；先前命名的 C（普通）、O（普通）和 N（坏死）组。还有另外两组不同的分离株，它们都是重组的； R-1 分离株具有 N（5' 末端次要）和 O（主要）亲本，R-2 分离株具有 R-1（主要）和 N（3' 末端次要）亲本。许多分离株还具有额外的次要组内和组间重组基因组区域。通过使用同义密码子的分区序列逐步识别和去除重组体，解决了基因组之间复杂的相互关系。对来自非重组异时采样分离株的两个基因序列数据集（73 个非重组主要 ORF 和 166 个部分 ORF）进行最小二乘测年和 BEAST 分析，发现 TMRCA 估计值的 95% 置信区间在 1,000 CE 左右重叠（常见公元）。 我们试图通过将估计的系统发育日期与世界范围内采用马铃薯和其他 PVY 宿主作为农作物的历史事件进行比较来确定最准确的年代，但发现来自非马铃薯分离株（尤其是来自南美的分离株）的基因序列的更多证据是必需的。