The complete chloroplast genome sequence of the Tibetan herb Phlomoides rotata (Benth. ex Hook.f.) Mathiesen (Lamiaceae).

Phlomoides rotata (Benth. ex Hook.f.) Mathiesen is a perennial herb endemic to Qinghai-Tibet Plateau with important medicinal properties. Here, we sequenced and analyzed the complete chloroplast (cp) genome of P. rotata and reconstructed the phylogeny of P. rotata based on 24 cp genomes. The genome of P. rotata is 151,825 bp in length, including a large single-copy (LSC) region of 83,129 bp and a small single-copy (SSC) region of 17,398 bp. A total of 131 genes were identified, of which 86 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Phylogenetic analyses revealed that the species P. rotata is closely related to Phlomoides alpina with bootstrap support (BS) values of 100%. Overall, the genomic resources presented in this study will be beneficial for further studies on evolutionary patterns of P. rotata and its closely related species.

The complete chloroplast genome of Codonopsis convolvulacea subsp. vinciflora.

Codonopsis convolvulacea subsp. vinciflora is a commonly used and endangered herb in Tibetan medicine. The chloroplast genome was determined to be 187,634 bp in length and contained a large single-copy and a small single-copy region of 102,174 bp and 8552 bp, respectively. The genome is predicted to contain 140 genes, including 90 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 38.72%. A phylogenetic tree reconstructed by 11 chloroplast genomes reveals that Codonopsis convolvulacea subsp. vinciflora is mostly related to C. tsinglingensis with bootstrap support values of 100%.

Undibacterium crateris sp. nov., isolated from water of crater lake.

A Gram-stain-negative, aerobic, flagellated, non-spore-forming, rod-shaped bacterium, named B2R-29T, was isolated from water collected from a crater lake on Da Hinggan mountain, PR China. Strain B2R-29T was oxidase- and catalase-positive. On the basis of the results of 16S rRNA gene sequence analyses, strain B2R-29T clearly belonged to the family Oxalobacteraceae, class Betaproteobacteria and showed the highest similarity to Undibacterium oligocarboniphilum EM1T (97.4 %) and to the other species of Undibacterium (less than 96.8 %). In the phylogenetic tree, strain B2R-29T formed a clade with U. oligocarboniphilum EM1T and Undibacterium squillarum CMJ-9T, indicating that is a member of the genus Undibacterium. Digital DNA-DNA hybridization and average nucleotide identity analyses were performed and the values between strain B2R-29T and its closely related Undibacterium species were less than 75.1 % and 16.9 %, respectively. The chemotaxonomic data of B2R-29T were as follows: major uniquinone, Q-8; predominant polar lipids, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol; major fatty acids, C16 : 0 and summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c); predominant polyamines, putrescine, 2-hydroxyputrescine and spermidine. The DNA G+C content was 51.7 mol% from the genomic sequencing data. In accordance with the phenotypic, physiological and chemotaxonomic properties mentioned above, strain B2R-29T represents a novel species of the genus Undibacterium for which the name Undibacterium crateris sp. nov. is proposed. The type strain is B2R-29T (=CGMCC 1.13792T=KCTC 72018T).

Flavobacterium tibetense sp. nov., isolated from a wetland.

A novel, Gram-stain-negative, non-motile and rod-shaped bacterium, designated YH5T, was isolated from the YonghuCo wetland on the Tibetan Plateau. The strain was able to grow optimally with 1 % (w/v) NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6-9 (optimum pH 7) and 10-37 °C (optimum 30 °C). Vitamins were not required for growth. The major polar lipid of strain YH5T was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15 : 0, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Genome sequencing revealed a genome size of 2.74 Mbp and a G+C content of 33.3 mol%. Analysis of 16S rRNA gene sequences showed that strain YH5T belonged to the genus Flavobacterium, with the closest neighbours Flavobacterium luticocti xz20T (96.7 % similarity), Flavobacterium jejuense EC11T (96.4 %), Flavobacterium jumunjinense HME7102T (95.9 %) and Flavobacterium dongtanense LW30T (95.6 %). DNA-DNA relatedness between strain YH5T and the closest phylogenetically related strain F. luticocti xz20T was 27.0 %. Strain YH5T was clearly distinguished from the reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. Based on its phenotypic and chemotaxonomic characteristics, strain YH5T is classified as a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium tibetense sp. nov. is proposed. The type strain is YH5T (=CICC 24247T=KCTC 62174T).

Nitrincola tibetensis sp. nov., isolated from Lake XuguoCo on the Tibetan Plateau.

A novel Gram-stain-negative, motile and rod-shaped bacterium, designated xg18T, was isolated from Lake XuguoCo on the Tibetan Plateau. The strain was able to grow optimally at 0-2 % NaCl and tolerate up to 6 % NaCl. Growth occurred at pH 7.0-11.0 (optimum, pH 9.0-10.0) and 15-40 °C (optimum, 37 °C). Vitamins were not required for growth. The major polar lipids of strain xg18T were phosphatidyl ethanolamine and phosphatidylglycerol. The predominant respiratory quinone was Q-8. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The G+C content of genomic DNA was 46.1 mol%. Analysis of 16S rRNA sequences showed that strain xg18T belongs to the genus Nitrincola, with Nitrincola alkalisediminis MEB087T (KC822363, 98.6 %) as its closest neighbour. The DNA-DNA relatedness value of strain xg18T with its closest phylogenetic neighbour, N. alkalisediminis JCM 19317T, was 43.1±3.2 %. Strain xg18T was clearly distinguishable from the type strain of the genus Nitrincola through phylogenetic analysis, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain xg18T could be classified as a representative of a novel species of the genus for which the name Nitrincola tibetensis sp. nov. is proposed. The type strain is xg18T (=CICC 24457T=KCTC 62401T).