Marine genomics最新文献_第2页

Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds 对三种地中海海绵微生物组进行宏基因组比较分析，以确定参与生物活性化合物生物合成的基因

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-07-21 DOI: 10.1016/j.margen.2025.101202

Serena Federico , Roberta Esposito , Maria De Rosa , Michele Sonnessa , Sofia Reddel , Gaia Laurenzi , Marco Bertolino , Marco Giovine , Marina Pozzolini , Valerio Zupo , Maria Costantini

{"title":"Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds","authors":"Serena Federico , Roberta Esposito , Maria De Rosa , Michele Sonnessa , Sofia Reddel , Gaia Laurenzi , Marco Bertolino , Marco Giovine , Marina Pozzolini , Valerio Zupo , Maria Costantini","doi":"10.1016/j.margen.2025.101202","DOIUrl":"10.1016/j.margen.2025.101202","url":null,"abstract":"<div><div>Marine sponges host a range of microorganisms and among them, bacteria represent a significant part of their biomass. Furthermore, bacteria are promising sources of natural products to be applied in various fields. Often the study their biotechnological potential is relented by low grow rates. For this reason, such cultivation-independent approaches, as metagenomics tools applied to sponges is obtaining wide success. For the first time, here we aimed at having an almost complete information about taxonomic and functional diversity of bacteria associated to three sponges, <em>Agelas oroides</em>, <em>Haliclona</em> (<em>Halichoclona</em>) <em>vansoesti</em> and <em>Geodia cydonium</em>, previously reported as candidate sources of bioactive compounds for pharmacological, nutraceutical and cosmeceutical purposes. Comparative metagenomic analyses were applied, sequencing DNA from the three sponges by ONT GridION X5 Mk1 sequencer. Our findings revealed for all the analyzed sponges the presence of genes/enzymes responsible for the synthesis of vitamins, fatty acids, antioxidant glutathione, terpenes, steroids and carotenoids. Consequently, we demonstrated the three sponges under analysis and their associated microorganisms could be considered good candidates for the isolation and identification of bioactive compounds for biotechnological application in the field of pharmacology, nutraceuticals and cosmeceuticals as well as environmental biotechnologies. Overall, metagenomic data represent a useful tool exploitable to sustainably develop bioactive products.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101202"},"PeriodicalIF":1.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144672176","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}

引用次数: 0

Complete genome sequence of Vibrio sinus, a potential contributor to collagen degradation 窦弧菌的全基因组序列，胶原降解的潜在贡献者

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-07-09 DOI: 10.1016/j.margen.2025.101201

Dingyong Huang , Wanjia Tong , Jinfeng Wang , Jianjia Wang , Yan Zhuang , Peng Tian , Xiaolei Wang

{"title":"Complete genome sequence of Vibrio sinus, a potential contributor to collagen degradation","authors":"Dingyong Huang , Wanjia Tong , Jinfeng Wang , Jianjia Wang , Yan Zhuang , Peng Tian , Xiaolei Wang","doi":"10.1016/j.margen.2025.101201","DOIUrl":"10.1016/j.margen.2025.101201","url":null,"abstract":"<div><div>Collagenase is an enzyme that has been shown to be highly effective in the degradation of both native triple-helical collagen and its denatured form (<em>e.g.</em>, gelatin). As a virulence factor secreted by pathogenic bacteria (<em>Clostridium histolyticum</em>, <em>Vibrio</em>, <em>Bacillus cereus</em>), this efficacy is attributed to the unique ability of the enzyme to hydrolyze Gly-X-Y bonds within thermally stable fibrillar structures. A highly efficient gelatin degrading strain, <em>Vibrio sinus</em> S4M6<sup>T</sup>, was isolated from the surface seawater collected in Dongshan Bay (Fujian, PR China), but the key genes involved in gelatin degradation remain unknown. Here, we report the complete genome sequence of <em>Vibrio sinus</em> S4M6<sup>T</sup> and its collagen degrading genes. The genome of strain S4M6<sup>T</sup> consists of two circular chromosomes, with a total chromosome length of 4.78 Mbp and a GC content of 43.4 %. Genomic analysis revealed that strain S4M6<sup>T</sup> encodes a collagenase gene involved in collagen degradation. This study provides a genetic insight of collagen degradation in marine <em>Vibrio</em> species.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101201"},"PeriodicalIF":1.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578852","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}

引用次数: 0

Complete genome sequence of Alteromonas sp. OM2203, a marine bacterium degrading Ulva prolifera polysaccharides 降解浒苔多糖的海洋细菌Alteromonas sp. OM2203的全基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-05-16 DOI: 10.1016/j.margen.2025.101198

Ming-Chen Wang , Zhi-Qing Wang , Jia-Rong Liu , Na Wang , Zhen-Kun Li , Fei-Fei Li , Yu-Han Sang , Hui-Hui Fu

引用次数: 0

De novo assembly and annotation of the pantranscriptome of Astyanax lacustris on the liver and pituitary-gonadal axis 湖astanax lastris肝脏和垂体性腺轴全转录组的从头组装和注释

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-04-16 DOI: 10.1016/j.margen.2025.101190

David Aciole Barbosa , Giovana Souza Branco , Aline Dal'Olio Gomes , Carlos Eduardo Tolussi , Marcela Muñoz-Peñuela , Bruno C. Araújo , Iuri Batista da Silva , Renata Guimarães Moreira , Luiz R. Nunes , Fabiano B. Menegidio

{"title":"De novo assembly and annotation of the pantranscriptome of Astyanax lacustris on the liver and pituitary-gonadal axis","authors":"David Aciole Barbosa , Giovana Souza Branco , Aline Dal'Olio Gomes , Carlos Eduardo Tolussi , Marcela Muñoz-Peñuela , Bruno C. Araújo , Iuri Batista da Silva , Renata Guimarães Moreira , Luiz R. Nunes , Fabiano B. Menegidio","doi":"10.1016/j.margen.2025.101190","DOIUrl":"10.1016/j.margen.2025.101190","url":null,"abstract":"<div><div><em>Astyanax lacustris</em> is a model of laboratory native fish species. Reproductive studies of this species have already been performed. Nevertheless, there is a relative shortcoming of gene sequence information available in public databases, which hinder their use in more comprehensive investigations that employ sensitivity molecular biology techniques to assess gene expression profile for biomarker identification. In this data article, we report the first <em>de novo</em> transcriptome assembly of <em>A. lacustris</em> testicles, ovaries and male / female pituitary gland improving gene sequence data available for this fish species and transcriptome of male liver. Illumina sequencing generated 808,023,356 raw reads, filtered in 752,739,866 high-quality reads. Initially, a <em>de novo</em> assembly was filtered to include protein coding elements only in each tissue sample, which were merged in a final pantranscriptome (PAN) containing 109,232 contigs. The PAN was functionally annotated against a custom Actinopterygii proteins dataset and EggNOG terms with the aid of EnTAP, retrieving homology queries for about 90 % of all transcripts. Therefore, in this study we provide a PAN and a custom blast tool that can help discovery genomic information on metabolism pathways and their related genes in <em>A. lacustris</em>, enabling future research and molecular studies using this fish species as a model.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"81 ","pages":"Article 101190"},"PeriodicalIF":1.3,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835173","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}

引用次数: 0

A “light in the darkness”: First transcriptomic data from deep-sea spiny eels (Notacanthus, Notacanthiformes) “黑暗中的光”：深海棘鳗（Notacanthus, Notacanthiformes）的首个转录组学数据

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-02-18 DOI: 10.1016/j.margen.2025.101182

André Gomes-dos-Santos , André M. Machado , Francisco Baldó , Juan Carlos Arronte , L. Filipe C. Castro , David Barros-García

引用次数: 0

Genomic analysis of Vibrio sp. D3 reveals its role in marine sulfur cycling 弧菌 D3 的基因组分析揭示了其在海洋硫循环中的作用D3 揭示其在海洋硫循环中的作用

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-02-12 DOI: 10.1016/j.margen.2025.101181

Fei-Fei Li , Zhen-Kun Li , Ming-Chen Wang , Jia-Rong Liu , Na Wang , Zhi-Qing Wang , Yu-Zhong Zhang , Hui-Hui Fu

{"title":"Genomic analysis of Vibrio sp. D3 reveals its role in marine sulfur cycling","authors":"Fei-Fei Li , Zhen-Kun Li , Ming-Chen Wang , Jia-Rong Liu , Na Wang , Zhi-Qing Wang , Yu-Zhong Zhang , Hui-Hui Fu","doi":"10.1016/j.margen.2025.101181","DOIUrl":"10.1016/j.margen.2025.101181","url":null,"abstract":"<div><div>Dimethylsulfoniopropionate (DMSP) is an important organosulfur compound, with key roles in global carbon and sulfur cycling, stress tolerance, chemotaxis, and, potentially, climate regulation. The strain <em>Vibrio</em> sp. D3 was isolated from the surface seawater samples in Qingdao coastal area, which could grow on DMSP as sole carbon source. Here, we report the complete genome sequence of strain D3 and analyzed its genomic characteristics related to the sulfur metabolism, especially DMSP. The genome of strain D3 contains two circular chromosomes of total 5,104,020 bp with a mean GC content of 44.87 %. DMSP transporter gene <em>bccT</em> and acryloy-CoA reductase gene <em>acuI</em>, which is essential in DMSP cleavage, are identified in the genome of <em>Vibrio</em> sp. D3. Potential DMSP demethylase gene <em>dmdA</em> (26.07 %, amino acid sequence identity) and DMSP lyase gene <em>dddX</em> (26.32 %, amino acid sequence identity) are predicted in the genome of strain D3, whose functions need further experimental verification. <em>Vibrio</em> sp. D3 also contains <sub><em>L</em></sub>-Met gamma-lyase (MegL) to generate MeSH from <sub><em>L</em></sub>-Met and complete assimilatory sulfate reduction pathway. Together, the genome of strain D3 reveals the possible DMSP catabolic pathways and supports its role in sulfur cycling.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101181"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387294","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}

引用次数: 0

Genomics analysis of Vreelandella piezotolerans V23 reveals its role in D-amino acids metabolism 对压耐受性V23的基因组学分析揭示了其在d -氨基酸代谢中的作用

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-02-12 DOI: 10.1016/j.margen.2025.101179

Dan Liu, Tie-Ji Gu, Hou-Qi Wang, Ze-Kun Liu, Meng-Qi Wang, Jing-Li Lü, Xin-Yi Wang, Peng Wang, Chen Wang

{"title":"Genomics analysis of Vreelandella piezotolerans V23 reveals its role in D-amino acids metabolism","authors":"Dan Liu, Tie-Ji Gu, Hou-Qi Wang, Ze-Kun Liu, Meng-Qi Wang, Jing-Li Lü, Xin-Yi Wang, Peng Wang, Chen Wang","doi":"10.1016/j.margen.2025.101179","DOIUrl":"10.1016/j.margen.2025.101179","url":null,"abstract":"<div><div>D-amino acids are generally supposed to be unique metabolites existing only in bacteria. They can not only modify the bacterial cell wall and promote plant growth, but also participate in the immune regulation of mammals, which is of great significance in nature. <em>Vreelandella piezotolerans</em> V23, a Gram-negative and aerobic bacterium, was isolated from coastal seawater of the Yellow Sea, China. Here, we report the genome of strain V23 and its genomic characteristics to utilize D-amino acids. The genome of strain V23 consists of a single circular chromosome with a size of 3,926,051 bp and a GC content of 58.11 %. Genomic analysis revealed that strain V23 possessed various genes responsible for D-amino acids metabolism and a pathway of synthesizing peptidoglycan from D-amino acids. The results indicated that strain V23 has the capacity to utilize D-amino acids. And strain V23 has been confirmed to be able to grow up with different D-amino acids as the sole nitrogen source. This study also enhances our understanding of the physiological and metabolic characteristics, interspecific diversity of strains of <em>Vreelandella</em> genus, and provides a crucial foundation for further investigation of D-amino acids metabolism.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101179"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143395373","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}

引用次数: 0

Genomic insights into Marinobacterium sediminicola CGMCC 1.7287T: A polyhydroxyalkanoate-producing bacterium isolated from marine sediment 沉积海洋细菌CGMCC 1.7287T：一种从海洋沉积物中分离的聚羟基烷酸盐生产细菌的基因组研究

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-02-12 DOI: 10.1016/j.margen.2025.101180

Meng-Ru Wang, Yuke Zhang, Zheng-Jun Li

{"title":"Genomic insights into Marinobacterium sediminicola CGMCC 1.7287T: A polyhydroxyalkanoate-producing bacterium isolated from marine sediment","authors":"Meng-Ru Wang, Yuke Zhang, Zheng-Jun Li","doi":"10.1016/j.margen.2025.101180","DOIUrl":"10.1016/j.margen.2025.101180","url":null,"abstract":"<div><div>Polyhydroxyalkanoate (PHA) is a promising polyester with superior properties including biodegradability, biocompatibility, and biorenewability. <em>Marinobacterium sediminicola</em> CGMCC 1.7287<sup>T</sup>, isolated from marine sediment in the East China Sea, has been found capable of producing PHA using volatile fatty acids as cost-effective substrates. Here, we report the genomic characteristics of <em>M. sediminicola</em> CGMCC 1.7287<sup>T</sup>, which possesses a circular chromosome of 3,554,135 bp with a GC content of 56.10 %. Gene annotation analysis revealed that the bacterium harbors enzymes involved in volatile fatty acids utilization, PHA synthesis, and ectoine accumulation. The presence of genes associated with ectoine synthesis suggests that this bacterium has stress resistance and cellular protection mechanism to adapt to saline environments. The genomic features provide important references for further genetic engineering of marine bacteria to effectively utilize volatile fatty acids for PHA production and enhance stress tolerance through ectoine accumulation.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101180"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387889","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}

引用次数: 0

Genomic analysis of Marinobacter flavimaris ZYH30 reveals its role in marine dimethylsulfide cycling 海洋黄杆菌ZYH30基因组分析揭示其在海洋二甲硫循环中的作用

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-01-31 DOI: 10.1016/j.margen.2025.101178

Liyan Liu , Hai Shi , Zihua Guo , Xiaotong Zhang , Xueqi Li , Xiao-Hua Zhang , Yunhui Zhang

{"title":"Genomic analysis of Marinobacter flavimaris ZYH30 reveals its role in marine dimethylsulfide cycling","authors":"Liyan Liu , Hai Shi , Zihua Guo , Xiaotong Zhang , Xueqi Li , Xiao-Hua Zhang , Yunhui Zhang","doi":"10.1016/j.margen.2025.101178","DOIUrl":"10.1016/j.margen.2025.101178","url":null,"abstract":"<div><div>Dimethylsulfide (DMS) is a volatile organic compound that influences climate change and plays a key role in the global sulfur cycle and chemotaxis. Marine bacteria can produce DMS from dimethylsulfoniopropionate (DMSP) and other sulfur precursors. A highly efficient DMS-producing strain, <em>Marinobacter flavimaris</em> ZYH30, was isolated from the surface sediment of the South China Sea, but the key genes involved in DMS production in its genome remain unknown. Here, we reported the complete genome sequence of <em>M. flavimaris</em> ZYH30 and its genomic potential in DMS cycling. The genome of <em>M. flavimaris</em> ZYH30 consists of a circular chromosome with a length of 4,631,282 bp and its GC content is 57.26 %. Genomic analysis showed that strain ZYH30 possesses a set of genes involved in DMS cycling, including a DMSP lyase DddL. In addition, <em>M. flavimaris</em> ZYH30 contained a <em>mddH</em> gene involved in hydrogen sulfide (H<sub>2</sub>S) and methanethiol (MeSH) dependent DMS production pathways. This study provides genetic insights into the DMS production processes and sulfur cycling in marine sediment bacteria.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101178"},"PeriodicalIF":1.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158637","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}

引用次数: 0

Complete genome sequence of Alteromonas marina OM2201, a marine bacterium degrading Ulva prolifera polysaccharides isolated from surface of the Yellow Sea 从黄海表面分离的降解增生Ulva多糖的海洋细菌Alteromonas marina OM2201的全基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2025-01-25 DOI: 10.1016/j.margen.2025.101168

Shi-Ning Cai , Hai-Xia Zhu , Zhi-Gang Tang , Xue-Yun Geng , Mei-Ling Sun

{"title":"Complete genome sequence of Alteromonas marina OM2201, a marine bacterium degrading Ulva prolifera polysaccharides isolated from surface of the Yellow Sea","authors":"Shi-Ning Cai , Hai-Xia Zhu , Zhi-Gang Tang , Xue-Yun Geng , Mei-Ling Sun","doi":"10.1016/j.margen.2025.101168","DOIUrl":"10.1016/j.margen.2025.101168","url":null,"abstract":"<div><div>As a consequence of marine eutrophication, there has been an exponential growth of <em>Ulva prolifera</em>, culminating in the yearly emergence of a massive green tide along the shores of Qingdao. This phenomenon exerts a detrimental impact on the marine ecosystem. As reported, the expression level of <em>Alteromonas</em> enzymes involved in <em>U. prolifera</em> polysaccharides degradation is increased during the green tide outbreak period, potentially accelerating the breakdown of <em>U. prolifera</em> biomass. This enhanced degradation could facilitate the transition to the waning phase of the green tide event. In this study, strain <em>Alteromonas marina</em> OM2201 was isolated from seawater samples taken during an <em>U. prolifera</em> bloom in the coastal waters of Qingdao. Its genome contains a ring chromosome and two plasmids. The length of the circular chromosome was 4,489,073 bp with GC content of 44.21 mol%, and the length of plasmid 1 was 233,636 bp with GC content of 42.24 mol%, and the length of plasmid 2 was 5594 bp with GC content of 39.61 mol%. Genomic analysis showed that <em>Alteromonas marina</em> OM2201 contained a variety of ulvan lyase genes, indicating that it could promote the degradation of <em>U. prolifera</em> polysaccharides. This genetic makeup potentially enables the strain to expedite the decomposition of <em>U. prolifera</em> biomass. Therefore, this study broadens our understanding of the <em>Alteromonas</em> bacteria that can degrade <em>U. prolifera</em> polysaccharides during the outbreak period.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101168"},"PeriodicalIF":1.3,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158638","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}

引用次数: 0