Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101032
Manar El Samak , Samira Zakeer , Amro Hanora , Samar M. Solyman
{"title":"Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community","authors":"Manar El Samak , Samira Zakeer , Amro Hanora , Samar M. Solyman","doi":"10.1016/j.margen.2023.101032","DOIUrl":"10.1016/j.margen.2023.101032","url":null,"abstract":"<div><p>Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge <em>Theonella</em> sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101032"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9673955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101044
Thendo S. Tshilate , Edson Ishengoma , Clint Rhode
{"title":"A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance","authors":"Thendo S. Tshilate , Edson Ishengoma , Clint Rhode","doi":"10.1016/j.margen.2023.101044","DOIUrl":"10.1016/j.margen.2023.101044","url":null,"abstract":"<div><p><em>Haliotis midae</em> or “<em>perlemoen</em>” is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of <em>H. midae</em> should assist in minimising the pressure on the wild populations. Here, the draft genome of <em>H. midae</em> has been sequenced, assembled, and annotated. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238 Mb, scaffold N50 of 0. 238 Mb and GC level of 40%. Gene annotation, combining <em>ab initio</em> and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (<em>H. laevigata, H. rubra, H. discus hannai</em> and <em>H. rufescens</em>) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that <em>H. midae</em> is closely related to the Australian Greenlip (<em>H. laevigata</em>) and Blacklip (<em>H. rubra</em>). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101044"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9737332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101045
Xiao-Lan Yue , Lin Xu , Li Cui , Ge-Yi Fu , Xue-Wei Xu
{"title":"Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean","authors":"Xiao-Lan Yue , Lin Xu , Li Cui , Ge-Yi Fu , Xue-Wei Xu","doi":"10.1016/j.margen.2023.101045","DOIUrl":"10.1016/j.margen.2023.101045","url":null,"abstract":"<div><p>Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon<strong>-</strong>fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood–Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla <em>Pseudomonadota</em> and <em>Desulfobacterota</em>. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order <em>Rhodothermales</em> and the family <em>Hyphomicrobiaceae</em>. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101045"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101046
Minji Kim, Soo-Je Park
{"title":"Complete genome sequence of Halomonas alkaliantarctica MSP3 isolated from marine sediment, Jeju Island","authors":"Minji Kim, Soo-Je Park","doi":"10.1016/j.margen.2023.101046","DOIUrl":"10.1016/j.margen.2023.101046","url":null,"abstract":"<div><p>As a moderate halophilic-heterotrophic bacterium, <em>Halomonas alkaliantarctica</em> MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes (61 tRNA and 18 rRNA). According to the genome annotation, it was revealed that the strain MSP3 harbors genes encoding for urease and urea transporters, which play a crucial role in the process of urea degradation and utilization. In addition, it is noteworthy that the MSP3 strain possesses genes encoding for both cytochrome <em>c</em> oxidase and cytochrome <em>bd</em> oxidase, thereby conferring upon it the ability to adapt to various levels of oxygen (oxic to microoxic) and to execute denitrification processes in the absence of oxygen. Moreover, it was observed that strain MSP3 had genes for the glyoxylate cycle, which is an alternative pathway to the TCA cycle. Furthermore, it was observed that the MSP3 strain exhibited the ability to thrive across a diverse spectrum of NaCl concentrations, ranging from 2% to 10% (<em>w</em>/<em>v</em>). Collectively, strain MSP3 may possess an advantage over competitors within the marine ecosystem, particularly in conditions where carbon substrates are restricted. The genomic-based assumption could potentially be substantiated by the presence of a multitude of transporter genes within the genome.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101046"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10041771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101043
Min Zhang , Xiao-Di Wang , Yue Lin , Shu-Yan Wang , Shan Zhang , Jin Cheng , Mei-Ling Sun , Peng Wang , Hui-Hui Fu , Chun-Yang Li , Nan Zhang
{"title":"Genomic analysis of Marinomonas algicola SM1966T reveals its role in marine sulfur cycling","authors":"Min Zhang , Xiao-Di Wang , Yue Lin , Shu-Yan Wang , Shan Zhang , Jin Cheng , Mei-Ling Sun , Peng Wang , Hui-Hui Fu , Chun-Yang Li , Nan Zhang","doi":"10.1016/j.margen.2023.101043","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101043","url":null,"abstract":"<div><p>Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. <em>Marinomonas algicola</em> SM1966<sup>T</sup>, a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of <em>Ulva pertusa</em> (Chlorophyta) algal sample collected off the coastal areas of Rongcheng, China. Here, we report the complete genome sequence of strain SM1966<sup>T</sup> and its genomic characteristics to utilize DMSP, which may be produced by <em>Ulva pertusa.</em> The genome of strain SM1966<sup>T</sup> contains one circular chromosome (4.3 Mbp) and one circular plasmid (149,271 bp). Genomic analysis showed that strain SM1966<sup>T</sup> possesses a set of genes involved in DMSP transport, DMSP cleavage and the catabolism of acrylate, one product of DMSP cleavage. The results indicated that strain SM1966<sup>T</sup> has the capacity to utilize DMSP and produce dimethyl sulfide (DMS), a volatile infochemical with important roles in global sulfur cycling. This study provides genetic insights into DMSP catabolism by algae-associated bacteria.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101043"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49855077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-08-01DOI: 10.1016/j.margen.2023.101033
Suzhen Li , Yong-Jun Jiang , Zhongjun Ma , Nan Wang
{"title":"Complete genome sequence of Streptomyces sp. HNA39, a new cyclizidine producer isolated from a South China Sea sediment","authors":"Suzhen Li , Yong-Jun Jiang , Zhongjun Ma , Nan Wang","doi":"10.1016/j.margen.2023.101033","DOIUrl":"10.1016/j.margen.2023.101033","url":null,"abstract":"<div><p><em>Streptomyces</em> sp. HNA39 is a promising candidate for the production of antineoplastic metabolites screened from a collection of 448 actinomycetes derived from coastal sediments. The complete genome sequence of HNA39 comprises a 7,351,753-bp linear chromosome with a GC content of 71.94%. Whole genome analysis reveals the presence of 29 putative biosynthetic gene clusters (BGCs) encoding secondary metabolites. Among them, a type I PKS BGC shows an 82% similarity with the cyclizidine (CLD) BGC identified from <em>Streptomyces</em> NCIB 11649. LC-MS profiles further supported the production of new CLD congeners. Bafilomycins were also found produced in abundance, corresponding to another type I PKS BGC highly homologous to that of bafilomycin B1 from <em>S. lohii</em>. CLDs are indolizidine alkaloids consisting a fused five- and six-membered ring system with an intriguing cyclopropane terminal linked by a <em>trans</em>-dienic chain. The cyclization mechanism of the cylopropyl ring, one of its pharmacophores, is still unknown. Genome sequencing of the new CLD producer and subsequent comparative analysis of their gene clusters would further our understanding of the chemistry behind cyclopropane formation.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"70 ","pages":"Article 101033"},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10041770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223T, isolated from bathypelagic seawater","authors":"Jin-Cheng Rong, Li Sheng, Li-Hua Jiang, Mao-Li Yi, Jin-Ying Wu, Qi Zhao","doi":"10.1016/j.margen.2023.101031","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101031","url":null,"abstract":"<div><p>During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus <em>Hyphococcus</em>. The type strain, <em>Hyphococcus flavus</em> MCCC 1K03223<sup>T</sup>, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223<sup>T</sup> is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of <em>H. flavus</em> revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"69 ","pages":"Article 101031"},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49855181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-06-01DOI: 10.1016/j.margen.2023.101030
Engy Mahmoud, Amro Hanora, Salah Abdalla, Ali A. Abdelrahman Ahmed, Samira Zakeer
{"title":"Shotgun metagenomic analysis of bacterial symbionts associated with “Chromodoris quadricolor” mantle","authors":"Engy Mahmoud, Amro Hanora, Salah Abdalla, Ali A. Abdelrahman Ahmed, Samira Zakeer","doi":"10.1016/j.margen.2023.101030","DOIUrl":"10.1016/j.margen.2023.101030","url":null,"abstract":"<div><p>Nudibranchs are colorful marine invertebrates having a diverse group of understudied animals. Recently, some nudibranch members have acquired some attention while others still have not. <em>Chromodoris quadricolor</em> is a member of the Red Sea nudibranch, which did not have the chance to get significant attention. Unlike various invertebrates, it lacks a shell suggesting that it must defend itself in other ways. Therefore, in the present study, we were concerned about the mantle-associated bacterial communities. Being essential partners of this dorid nudibranch system, we investigated their taxonomic and functional profiles. We performed a whole metagenomic shotgun approach for the mantle bacterial cells after a differential pelleting procedure. In this procedure, we separated most of the prokaryotic cells from the eukaryotic host cells. Our findings showed that the mantle-body part holds a diverse group of bacterial species relating mainly to <em>Proteobacteria</em> and <em>Tenericutes</em> phyla. There were novel findings regarding the bacterial members associated with the nudibranch mollusks group. Various species were not previously recorded as bacterial symbionts with nudibranchs. Those members were <em>Bathymodiolus brooksi thiotrophic gill symbiont</em> (23.2%), <em>Mycoplasma marinum</em> (7.4%), <em>Mycoplasma todarodis</em> (5%), <em>and Solemya velum gill symbiont</em> (2.6%). The presence of these bacterial species assumed a nutritional role to the host. However, some of these species were present in a high abundance, suggesting their important symbiosis with <em>Chromodoris quadricolor</em>. In addition, exploring the bacterial ability to produce valuable products resulted in the prediction of 2088 biosynthetic gene clusters (BGCs). We identified different gene cluster classes. Polyketide BGC class was the most represented. Others were related to fatty acid BGCs, RiPP, saccharide, terpene, and NRP BGC classes. Prediction of the activity of these gene clusters resulted in, mainly, an antibacterial activity. In addition, different antimicrobial secondary metabolites were also detected. These secondary metabolites are considered key components regulating the bacterial species interactions in their ecosystem. This suggested the significant contribution of these bacterial symbionts to protect the nudibranch host against predators and pathogens. Globally, it is the first detailed study concerned with both the taxonomic diversity and functional potentials of the bacterial symbionts associated with <em>Chromodoris quadricolor</em> mantle.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"69 ","pages":"Article 101030"},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9348792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2023-06-01DOI: 10.1016/j.margen.2023.101029
Xuan Zou, Chuan-Lei Suo, Xiao-Mei Geng, Chun-Yang Li, Hui-Hui Fu, Yi Zhang, Peng Wang, Mei-Ling Sun
{"title":"Complete genome sequence of Bacillus cereus 2-6A, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Pacific Ocean","authors":"Xuan Zou, Chuan-Lei Suo, Xiao-Mei Geng, Chun-Yang Li, Hui-Hui Fu, Yi Zhang, Peng Wang, Mei-Ling Sun","doi":"10.1016/j.margen.2023.101029","DOIUrl":"10.1016/j.margen.2023.101029","url":null,"abstract":"<div><p><em>Bacillus cereus</em> 2-6A, was isolated from the sediments in the hydrothermal area of the Pacific Ocean with a water depth of 2628 m. In this study, we report the whole genome sequence of strain 2-6A and analyze that to understand its metabolic capacities and biosynthesis potential of natural products. The genome of strain 2-6A consists of a circular chromosome of 5,191,018 bp with a GC content of 35.3 mol% and two plasmids of 234,719 bp and 411,441 bp, respectively. Genomic data mining reveals that strain 2-6A has several gene clusters involved in exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) production and complex polysaccharides degradation. It also possesses a variety of genes for allowing strain 2-6A to cope with osmotic stress, oxidative stress, heat shock, cold shock and heavy metal stress, which could play a vital role in the adaptability of the strain to hydrothermal environments. Gene clusters for secondary metabolite production, such as lasso peptide and siderophore, are also predicted. Therefore, genome sequencing and data mining provide insights into the molecular mechanisms of <em>Bacillus</em> in adapting to hydrothermal deep ocean environments and can facilitate further experimental exploration.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"69 ","pages":"Article 101029"},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9356795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench","authors":"Yoshihito Nikaidou , Yong Guo , Mahoko Taguchi , Shigeru Chohnan , Tomoyasu Nishizawa , Yasurou Kurusu","doi":"10.1016/j.margen.2023.101028","DOIUrl":"10.1016/j.margen.2023.101028","url":null,"abstract":"<div><p>Herein, we report the complete genome sequence of <em>Pseudoalteromonas</em> sp. PS1M3 (= NCBI <span>87791</span><svg><path></path></svg>), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs. The genome of PS1M3 had a total size of 4,351,630 bp, an average GC content of 39.9%, and contained a total of 3811 predicted protein coding sequences, 28 rRNAs, and 100 tRNAs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was utilized to annotate the genes and KofamKOALA within KEGG assigned a gene cluster involved in glycogen biosynthesis and metabolic pathways with regard to heavy metal resistance (copper; <em>cop</em> and mercury; <em>mer</em>), indicating that PS1M3 can potentially use a stored glycogen as an energy source under oligotrophic environment and cope with multi-heavy metal contamination. To assess available genome relatedness indices, whole-genome average nucleotide identity analysis was examined using the complete genome sequences of <em>Pseudoalteromonas</em> spp., showing that 67.29–97.40% sequence similarity with PS1M3. This study may be useful in understanding the roles of a psychrotrophic <em>Pseudoalteromonas</em> in cold deep-sea sediment adaptation mechanisms.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"69 ","pages":"Article 101028"},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9356797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}