Genome-based classification of members in the genus Actinoplanes and its closely related genera and description of Actinoplanes oryzae sp. nov. and reclassification of Couchioplanes caeruleus subsp. azureus as Couchioplanes azureus sp. nov.

Members of the genus <i>Actinoplanes</i> and six closely related genera were classified based on their genomic data, including the aa identity value threshold and the position on the phylogenomic trees and 16S rRNA gene phylogenetic trees. We suggested that <i>Couchioplanes</i>, <i>Nucisporomicrobium</i> and <i>Pseudosporangium</i> should be reclassified as the genus <i>Actinoplanes</i> on their genome-based classification. However, the phenotypic data of these three genera remains unclear and requires more closely related strains of these genera to confirm their taxonomic position in the future. The diaminopimelic acid (DAP) of <i>Actinoplanes</i> was <i>meso</i>-DAP or <i>meso</i>-DAP and 3<i>OH</i>-DAP, while Nucisporomicrobium contained <i>meso</i>-DAP. The genus <i>Couchioplanes</i> contains l-lysine, and <i>Pseudosporangium</i> contains <i>meso-</i>DAP and 3<i>OH</i>-DAP. <i>Actinoplanes</i> and these three genera contained MK-9(H₄) or MK-9(H₆) being the major menaquinones. The major fatty acids of these genera were <i>anteiso</i>- and <i>iso</i>-branched, and their polar lipids comprised phosphatidylethanolamine. Moreover, <i>Couchioplanes caeruleus</i> subsp. <i>azureus</i> was reclassified as <i>Couchioplanes azureus</i> comb. nov. In addition, an endophytic actinobacterium, strain RD1^T, isolated from the leaf sample of a Jasmine rice plant (<i>Oryza sativa</i>) in Thailand has been classified. This strain is an aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce poly-sporous-tubular sporangia, and spores are motile. Strain RD1^T shared 98.9% of 16S rRNA gene similarity with <i>Nucisporomicrobium flavum</i> NEAU-24^T. <i>Actinoplanes lichenis</i> TISTR 2343^T shared the highest digital DNA-DNA hybridization, average nucleotide identity blast and average nucleotide identity MUMmer, with values of 40.9%, 89.8% and 91.2%, respectively. The genotypic and chemotaxonomic data confirmed that strain RD1^T belonged to the genus <i>Actinoplanes</i> and was recognized as a novel species named <i>Actinoplanes oryzae</i> sp. nov. The type strain is RD1^T (=TBRC 17751^T=NRRL B-65688^T). Genome mining of strain RD1^T revealed the biosynthetic genes encoding proteins related to antibiotic production and plant growth promotion.