Department of Biomedical Engineering, One Shields Ave, University of California, Davis, CA 95616, USA.
Genome Center, One Shields Ave, University of California, Davis, CA 95616, USA.
Viruses. 2018 Oct 20;10(10):576. doi: 10.3390/v10100576.
Chloroviruses (family ) are dsDNA viruses found throughout the world's inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic "contexts", the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed "gene gangs". Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression.
噬藻体病毒（科）是一种双链 DNA 病毒，广泛存在于世界各地的内陆水域中。对 41 种噬藻体病毒（每个基因组约 330±40kbp）的基因组中的开放阅读框进行了分析，以寻找进化保守的局部基因组“上下文”的证据，即将生物信息组织成大于基因规模的单位。尽管病毒类型之间普遍失去了同线性，但我们通过信息学方法检测到了一个高度保守的基因组上下文，该上下文由三个或更多基因组成的群组定义，我们称之为“基因帮”。与以前描述的局部基因组上下文不同，基因帮的定义只要求成员基因始终位于同一位置，不受链、调控位点或间隔序列的限制（因此代表了一种新的保守结构基因组元件）。对功能注释和转录组数据的分析表明，一些基因帮可能组织了参与特定生化过程的基因，但这种组织不涉及它们的协调表达。
