Bean yellow mosaic virus (BYMV) is an economic potyvirus with worldwide distribution and a broad host range. Recently, phylogenetic studies of BYMV isolates have indicated the importance of comparing the full genome sequences to obtain a reliable classification. However, most available isolates in public databases are partially sequenced, and virologists continue to prefer partial genomes or individual genes for phylogenetic studies. As such, to avoid unbiased classification, phylogenetic studies should be based on either phylogenetic gene markers or a multigene dataset instead of just one random gene. In the present study, we sequenced the full genome of a BYMV isolate collected from an Iranian faba bean field using the Illumina Novaseq 6000 platform. The phylogenetic analysis revealed that the Iranian isolate is closely related to three isolates originating from faba bean fields in Japan, Australia and Germany. To identify the phylogenetic markers of BYMV, the topology distance between reconstructed trees based on individual genes and the whole genome was calculated using topology congruence tests considering only the topology of the compared trees and a character congruence test taking into account the characters, tree topology and estimated bootstrap support value. Accordingly, nuclear inclusion proteins a and b (NIa and NIb) and viral protein genome linked (VPg) were selected as evolutionary markers which can be used as appropriate representations of the full genome in phylogenetic studies. Furthermore, supermatrix approach was used to compare all BYMV isolates that have been fully or partially sequenced. The results demonstrate that all submitted BYMV strains can be divided into 10 main monophyletic clades with high bootstrap values; these are named BYM-1 through BYM-10 to avoid confusion with previously introduced nomenclature. Moreover, the results reveal that clustering based on phylogenetic analysis and their original host is not completely consistent, which supports recent phylogenetic studies based on available whole genome sequences.

豆黄花叶病毒（BYMV）是一种经济性的杯状病毒，在全球范围内都有广泛的传播范围。最近，BYMV分离株的系统发育研究表明，比较完整基因组序列以获得可靠分类的重要性。但是，公共数据库中大多数可用的分离株都进行了部分测序，病毒学家继续偏爱部分基因组或单个基因进行系统发育研究。因此，为了避免公正的分类，系统发育研究应基于系统发育基因标记或多基因数据集，而不仅仅是一个随机基因。在本研究中，我们使用Illumina Novaseq 6000平台对从伊朗蚕豆田收集的BYMV分离株的全基因组进行了测序。系统发育分析表明，伊朗分离株与源自日本，澳大利亚和德国蚕豆田的三种分离株密切相关。为了识别BYMV的系统发育标记，使用拓扑一致性测试来计算基于单个基因的重组树与整个基因组之间的拓扑距离，该拓扑一致性测试仅考虑比较树的拓扑，并考虑字符，树的拓扑结构和特征来进行字符一致性测试。引导程序估计支持值。因此，选择核内含蛋白a和b（NIa和NIb）以及病毒蛋白基因组连接（VPg）作为进化标记，可以用作系统发育研究中完整基因组的适当表示。此外，用supermatrix方法比较已全部或部分测序的所有BYMV分离株。结果表明，所有提交的BYMV菌株可分为10个具有高自举值的主要单系进化枝。这些名称分别称为BYM-1至BYM-10，以避免与先前引入的术语混淆。此外，结果表明基于系统发育分析的聚类与其原始宿主并不完全一致，这支持了基于可用全基因组序列的最新系统发育研究。