Genomics/technical resourcesComplete genome sequence of Serinicoccus sp. JLT9, an actinomycete isolated from the shallow-sea hydrothermal system
Introduction
Hydrothermal vents represent a unique habitat in the marine ecosystem and occur over a wide depth range, from the intertidal to the abyssal (Tarasov et al., 2005). Deep-sea hydrothermal systems are known to harbor numerous metabolically diverse microorganisms with potential biotechnological and environmental implications thus have received a great deal of attention (He and Zhang, 2016). However, comparatively few investigations on microbial community have been conducted in the shallow-sea hydrothermal systems (Tang et al., 2013). Shallow-sea hydrothermal systems (at the depth < 200 m) provide more instant access to investigate microbial genetic resource, which usually occur near active coastal or submarine volcanoes (Tang et al., 2013). The hydrothermal fluids vary greatly in their temperature, pH, and chemical composition due to subseafloor physical and chemical processes such as fluid-rock interactions, and the mixture of fluids and seawaters (Tarasov et al., 2005).
The genus Serinicoccus was a rare actinomycete taxon and the majority of isolates were collected at surface seawater and marine sediment (Traiwan et al., 2011, Xiao et al., 2011a, Yi et al., 2004). Marine actinomycete is underexploited source for the discovery of natural compounds (Bull et al., 2005). A potentially useful antitumor agent (seriniquinone) (Trzoss et al., 2014) and six bioactive compounds (Yang et al., 2013) were isolated from the representatives of the genus Serinicoccus. Here we present the complete genome sequence of Serinicoccus sp. JLT9. Serinicoccus sp. JLT9 was an aerobic, non-motile, non-sporulating, coccoid-shaped and yellow-colored, Gram-positive bacterium, which was obtained from the shallow-sea hydrothermal system, Kueishan Islet, offshore northeast of Taiwan. 16S rRNA gene in Serinicoccus sp. JLT9 showed 98% sequence similarity with that in Serinicoccus marinus DSM15273 (Yi et al., 2004) within the phylum Actinobacteria. To our knowledge, this study represents the first genome information of a cultivated actinomycete isolated from the shallow-sea hydrothermal system.
Section snippets
Data description
General features of Serinicoccus sp. JLT9 and the MIxS mandatory information were show in Table 1. Whole genome sequencing of Serinicoccus sp. JLT9 was accomplished using a hybrid approach (Koren et al., 2012), combining Illumina short read data (Illumina, USA) with PacBio long read data (Pacific Biosciences, USA). The genome sequences were de novo assembled by the HGAP2 program in the SMRT analysis server (v2.3). Illumina pair end reads were mapped to the assembled contigs to improve the
Nucleotide sequence accession numbers
The complete genome sequence of Serinicoccus sp. JLT9 (= JCM 31502T, = CGMCC 1.15779T) has been deposited at DDBJ/EMBL/GenBank under the accession number of CP014989.
Acknowledgments
This work was supported by the National Natural Science Foundation of China project (41276131 & 41676070), the National Program on Global Change and Air-Sea Interaction (GASI-03-01-02-05), MEL Internal Programs (MELRI1604), and the Fundamental Research Funds for the Central Universities (20720150078).
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2020, International Journal of Systematic and Evolutionary Microbiology