Department of Microbiology, Tuljaram Chaturchand College, Baramati 413 102, Maharashtra, India.
National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India.
Int J Syst Evol Microbiol. 2021 Jan;71(1). doi: 10.1099/ijsem.0.004591. Epub 2020 Dec 8.
Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with '. Phytoplasma cynodontis' strain BGWL-C1 followed by 97.65 % similarity with '. P. oryzae' strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to '. P. cynodontis', were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ' Phytoplasma sacchari' is proposed.
甘蔗丛枝病与稻黄矮植原体（16SrXI-B 组）有关，后者主要存在于印度次大陆和东南亚的甘蔗种植区。属于 16SrXI-B 组的甘蔗丛枝病植原体菌株的 16S rRNA 基因序列与 '. Phytoplasma cynodontis' 菌株 BGWL-C1 的相似度为 98.07%，其次与 '. P. oryzae' 菌株 RYD-J 的相似度为 97.65%。由于与系统发育上相关的物种明显分离，甘蔗丛枝病植原体的分类身份不清楚且令人困惑。我们试图根据 16S rRNA 基因（>1500bp）、9 个看家基因（>3500aa）、核心基因组系统发育（>10000aa）和 OGRI 值的系统发育分析来确定甘蔗丛枝病植原体的系统发育位置。获得了与 '. P. cynodontis' 密切相关的甘蔗丛枝病（菌株 SCGS）和百慕大草白叶病（BGWL）植原体（菌株 LW01）的草案基因组序列。SCGS 基因组由 29 个支架组成，对应于 505173bp，而 LW01 组装包含 21 个支架，对应于 483935bp，两个基因组的覆盖率均超过 330×，完整性均超过 90%。SCGS 的 G+C 含量为 19.86%，LW01 的 G+C 含量为 20.46%。菌株 SCGS 与菌株 LW01 的 orthoANI 值为 79.42%，dDDH 值为 22。总体分析表明，甘蔗丛枝病植原体在植原体的 RYD 组中形成一个遥远的分支。根据系统发育分析和从基因组序列获得的 OGRI 值，提出了一个新的分类单元'Phytoplasma sacchari'。
