Gan Han Ming, Lee Melvin V L, Savka Michael A
Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.
Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
PeerJ. 2019 Feb 8;7:e6366. doi: 10.7717/peerj.6366. eCollection 2019.
The reported DSM 30174 genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of B6, enabling for the first time, a proper comparative genomics of these contentious species. We provide concrete evidence that the previously reported type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that be reclassified as subsp. and that retains it species status with the proposed name of subsp. . This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both and into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that NCPPB3001 is sufficiently divergent from to propose two independent sub-clades. Third, demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than
所报道的DSM 30174基因组高度碎片化，阻碍了稳健的比较基因组学和基于基因组的分类分析。我们对模式菌株进行了重测序，生成了一个连续性大幅提高的基因组。此外，我们对B6的基因组进行了测序，首次实现了对这些有争议物种的恰当比较基因组学研究。我们提供了确凿证据，表明先前报道的模式菌株基因组（登录号：ASXY01）受到了污染，这解释了其异常大的基因组大小和碎片化组装。我们提议将[具体名称1]重新分类为[具体名称2]亚种，而[具体名称3]保留其物种地位，提议的名称为[具体名称4]亚种。该提议首先基于高成对基因组规模平均核苷酸同一性，支持将[具体名称1]和[具体名称3]合并为一个单一物种。其次，基于相关菌株间共享基因（核心基因）的串联比对构建的最大似然树表明，NCPPB3001与[具体名称3]有足够的差异，可提出两个独立的亚分支。第三，[具体名称3]显示出在其脂多糖中合成岩藻糖L构型的基因组潜力，这增强了其比[具体名称1]更有效地定殖于植物细胞的能力。
