Complete genome and data mining of Aeromicrobium sp. A1–2 isolated from the Southern Ocean

Liao, Li; Su, Shiyuan; Yu, Yong; Zhang, Jin; Chen, Bin

doi:10.1016/j.margen.2018.10.007

“…The complete genome of HQ09 T was sequenced on Ilumina Hiseq 4000 and PacBio RSII sequencing platforms at BGI Genomics Co. Two libraries were constructed for Illumina and PacBio sequencing, as previously [17, 18]. Clean sequences from PacBio sequencing were assembled using RS_HGAP Assembly3 in the SMRT Analysis v2.3.0 (https://github.com/PacificBiosciences/SMRT-Analysis) and corrected by Illumina sequences using soapSNP and soapIndel for the first round [19], and further checked using GATK pipeline (http://www.broadinstitute.org/gatk/).…”

Section: Genome Featuresmentioning

confidence: 99%

“…The complete genome of HQ09 T was sequenced on Ilumina Hiseq 4000 and PacBio RSII sequencing platforms at BGI Genomics Co. Two libraries were constructed for Illumina and PacBio sequencing, as previously [17,18]. Clean sequences from PacBio sequencing were assembled using RS_HGAP Assembly3 in the SMRT Analysis v2.3.0 (https:// github.…”

Section: Genome Featuresmentioning

confidence: 99%

Pseudopuniceibacterium antarcticum sp. nov., isolated from an Antarctic marine sponge

Liao

¹

,

Su

²

,

Zhang

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated strain HQ09T, was isolated from a marine sponge off the coast of Fields Peninsula, West Antarctica. Strain HQ09T grew at 4–35 °C (optimum, 25 °C), pH 5–9 (optimum, pH 7.0), and with 1–10% NaCl (optimum, 2 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain HQ09T was affiliated with the genus Pseudopuniceibacterium in the family Rhodobacteraceae , sharing 99.64 % identity with the type strain of Pseudopuniceibacterium sediminis , the only known species in the genus. However, the low digital DNA–DNA hybridization (dDDH) (27.2 %) and average nucleotide identity (ANI) (83.63 %) values between strain HQ09T and the type strain of Pseudopuniceibacterium sediminis indicated that they did not belong to the same species. Strain HQ09T could also be differentiated from Pseudopuniceibacterium sediminis by many phenotypic characteristics. The major fatty acids (>5 %) of strain HQ09T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), 11-methyl C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids included phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and one unidentified phospholipid. The predominant respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content was 62.63 mol%. Four secondary metabolite biosynthetic gene clusters were detected in the genome, potentially producing ectoine and three types of unknown compounds. On the basis of the polyphasic evidences obtained in this study, strain HQ09T represents a novel species of the genus Pseudopuniceibacterium , for which the name Pseudopuniceibacterium antarcticum sp. nov. is proposed, with the type strain being HQ09T (=KCTC 52229T=CGMCC 1.15538T).

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