Pub Date : 2025-08-28DOI: 10.1016/j.margen.2025.101214
Jun Li , Kun Liang , Ya Ma , Nan Zhang
Glutathione (GSH) is a well-known tripeptide composed of glutamic acid, cysteine and glycine. It plays critical roles in maintaining the redox homeostasis of cells and in cell cycle regulation, apoptosis, immunological defense, and pathological abnormalities. Caballeronia sp. DA-9, a Gram-negative and aerobic bacterium, was isolated from the sediment collected from the Weddell Sea. Here, we report the complete genome sequence of strain DA-9 and its genomic characteristics to synthesize and catabolize GSH. The genome of strain DA-9 contains three circular chromosomes and two plasmids. Genomic analysis showed that strain DA-9 contained a set of genes involved in GSH metabolism, indicating that it possesses the potential ability to synthesize and catabolize GSH. This study provides novel insights into GSH metabolism by marine microorganisms.
{"title":"Genomic analysis of Caballeronia sp. DA-9 reveals its role in glutathione metabolism","authors":"Jun Li , Kun Liang , Ya Ma , Nan Zhang","doi":"10.1016/j.margen.2025.101214","DOIUrl":"10.1016/j.margen.2025.101214","url":null,"abstract":"<div><div>Glutathione (GSH) is a well-known tripeptide composed of glutamic acid, cysteine and glycine. It plays critical roles in maintaining the redox homeostasis of cells and in cell cycle regulation, apoptosis, immunological defense, and pathological abnormalities. <em>Caballeronia</em> sp. DA-9, a Gram-negative and aerobic bacterium, was isolated from the sediment collected from the Weddell Sea. Here, we report the complete genome sequence of strain DA-9 and its genomic characteristics to synthesize and catabolize GSH. The genome of strain DA-9 contains three circular chromosomes and two plasmids. Genomic analysis showed that strain DA-9 contained a set of genes involved in GSH metabolism, indicating that it possesses the potential ability to synthesize and catabolize GSH. This study provides novel insights into GSH metabolism by marine microorganisms.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101214"},"PeriodicalIF":1.5,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144912106","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}
Pub Date : 2025-08-05DOI: 10.1016/j.margen.2025.101204
Huai-Ying Sun , Ji-Xiang Xin , Gen Li , Zhen-Yi Zhou , Xin Li , Hong Wang , Qun-Jian Yin , Bin Wei
Lysinibacillus sp. WB86 was isolated from a cold seep in the South China Sea, and its complete genome was sequenced using Oxford Nanopore Technologies (ONT). The genome consists of a single circular chromosome spanning 4,537,071 bp, with a G + C content of 37 %. FastANI analysis revealed a 99.38 % average nucleotide identity (ANI) with Lysinibacillus sphaericus A1, confirming its classification as a strain of L. sphaericus. Genome annotation identified 4397 protein-coding genes, along with 111 tRNAs and 34 rRNAs. Functional categorization using the COG database assigned 84.6 % of the protein-coding genes to specific roles, with the majority involved in transcription, amino acid transport and metabolism, translation and ribosomal biogenesis, and replication, recombination, and repair. Additionally, antiSMASH-based analysis uncovered eight biosynthetic gene clusters (BGCs), only one of which exhibited high similarity (>50 %) to known BGCs. This cluster was predicted to encode novel antimicrobial lanthipeptides, suggesting potential biotechnological applications.
{"title":"Complete genome sequence of Lysinibacillus sp. WB86, a potential antimicrobial lanthipeptides producer","authors":"Huai-Ying Sun , Ji-Xiang Xin , Gen Li , Zhen-Yi Zhou , Xin Li , Hong Wang , Qun-Jian Yin , Bin Wei","doi":"10.1016/j.margen.2025.101204","DOIUrl":"10.1016/j.margen.2025.101204","url":null,"abstract":"<div><div><em>Lysinibacillus</em> sp. WB86 was isolated from a cold seep in the South China Sea, and its complete genome was sequenced using Oxford Nanopore Technologies (ONT). The genome consists of a single circular chromosome spanning 4,537,071 bp, with a G + C content of 37 %. FastANI analysis revealed a 99.38 % average nucleotide identity (ANI) with <em>Lysinibacillus sphaericus</em> A1, confirming its classification as a strain of <em>L. sphaericus</em>. Genome annotation identified 4397 protein-coding genes, along with 111 tRNAs and 34 rRNAs. Functional categorization using the COG database assigned 84.6 % of the protein-coding genes to specific roles, with the majority involved in transcription, amino acid transport and metabolism, translation and ribosomal biogenesis, and replication, recombination, and repair. Additionally, antiSMASH-based analysis uncovered eight biosynthetic gene clusters (BGCs), only one of which exhibited high similarity (>50 %) to known BGCs. This cluster was predicted to encode novel antimicrobial lanthipeptides, suggesting potential biotechnological applications.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101204"},"PeriodicalIF":1.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779565","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}
Pub Date : 2025-07-28DOI: 10.1016/j.margen.2025.101203
Bin Jin , Xiao Liang , Xiaoyu Wang , Li-Hua Peng , Jin-Long Yang
Pseudoalteromonas, recognized as one of chitin decomposers in marine environments, plays a pivotal role in global carbon and nitrogen cycling. This study reports the whole genome sequence of bacterium M7NS11, which was isolated from deep-sea sediments of the New Britain Trench. Genomic analysis revealed two circular elements: a 3,607,764-bp chromosomal structure (41.79 % GC) and an 899,258-bp plasmid structure (40.87 % GC). Whole-genome analysis revealed that this strain possesses 9 genes encoding chitinases and 1 gene encoding lytic polysaccharide monooxygenase (LPMO), indicating that the strain may efficiently degrade chitin through synergistic interactions between chitinases and LPMO to acquire essential nutrients. Additionally, it contains four genes (amgK, glmU, murA, and murB), encoding enzymes which could utilize chitin degradation products to synthesize peptidoglycan, a major component of cell wall. The analysis of the complete genome of P. lipolytica M7NS11 provides new insights into the role of Pseudoalteromonas in deep-sea material cycling, and underscores the potential of P. lipolytica M7NS11 as a valuable resource for isolating efficient chitinases.
{"title":"Complete genome sequence of Pseudoalteromonas lipolytica M7NS11, a chitinolytic bacterium isolated from the New Britain Trench","authors":"Bin Jin , Xiao Liang , Xiaoyu Wang , Li-Hua Peng , Jin-Long Yang","doi":"10.1016/j.margen.2025.101203","DOIUrl":"10.1016/j.margen.2025.101203","url":null,"abstract":"<div><div><em>Pseudoalteromonas</em>, recognized as one of chitin decomposers in marine environments, plays a pivotal role in global carbon and nitrogen cycling. This study reports the whole genome sequence of bacterium M7NS11, which was isolated from deep-sea sediments of the New Britain Trench. Genomic analysis revealed two circular elements: a 3,607,764-bp chromosomal structure (41.79 % GC) and an 899,258-bp plasmid structure (40.87 % GC). Whole-genome analysis revealed that this strain possesses 9 genes encoding chitinases and 1 gene encoding lytic polysaccharide monooxygenase (LPMO), indicating that the strain may efficiently degrade chitin through synergistic interactions between chitinases and LPMO to acquire essential nutrients. Additionally, it contains four genes (<em>amgK</em>, <em>glmU</em>, <em>murA</em>, and <em>murB</em>), encoding enzymes which could utilize chitin degradation products to synthesize peptidoglycan, a major component of cell wall. The analysis of the complete genome of <em>P. lipolytica</em> M7NS11 provides new insights into the role of <em>Pseudoalteromonas</em> in deep-sea material cycling, and underscores the potential of <em>P. lipolytica</em> M7NS11 as a valuable resource for isolating efficient chitinases.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101203"},"PeriodicalIF":1.3,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144713441","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}
Pub Date : 2025-07-21DOI: 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
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, Agelas oroides, Haliclona (Halichoclona) vansoesti and Geodia cydonium, 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.
{"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}
Pub Date : 2025-07-09DOI: 10.1016/j.margen.2025.101201
Dingyong Huang , Wanjia Tong , Jinfeng Wang , Jianjia Wang , Yan Zhuang , Peng Tian , Xiaolei Wang
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 (e.g., gelatin). As a virulence factor secreted by pathogenic bacteria (Clostridium histolyticum, Vibrio, Bacillus cereus), 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, Vibrio sinus S4M6T, 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 Vibrio sinus S4M6T and its collagen degrading genes. The genome of strain S4M6T 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 S4M6T encodes a collagenase gene involved in collagen degradation. This study provides a genetic insight of collagen degradation in marine Vibrio species.
{"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}
Pub Date : 2025-05-16DOI: 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
Green algae Ulva prolifera cause successive green tides in the Yellow Sea, China, leading to harmful ecological impacts and economic losses. Bacterial degradation of U. prolifera polysaccharides could accelerate the breakdown of its biomass and transition to the waning phase of green tides. In this study, the strain Alteromonas sp. OM2203 was isolated from seawater samples in the coastal area of Qingdao during a U. prolifera bloom. The genome of strain OM2203 contains one circular chromosome totaling 4,556,409 bp, with a mean GC content of 44.05%. Genomic analysis revealed that Alteromonas sp. OM2203 contains 6 ulvan lyase genes, indicating its potential to degrade U. prolifera polysaccharides and expedite the decomposition of algal biomass. Collectively, the genome of Alteromonas sp. OM2203 provides insights into the role of Alteromonas bacteria in U. prolifera polysaccharide degradation.
{"title":"Complete genome sequence of Alteromonas sp. OM2203, a marine bacterium degrading Ulva prolifera polysaccharides","authors":"Ming-Chen Wang , Zhi-Qing Wang , Jia-Rong Liu , Na Wang , Zhen-Kun Li , Fei-Fei Li , Yu-Han Sang , Hui-Hui Fu","doi":"10.1016/j.margen.2025.101198","DOIUrl":"10.1016/j.margen.2025.101198","url":null,"abstract":"<div><div>Green algae <em>Ulva prolifera</em> cause successive green tides in the Yellow Sea, China, leading to harmful ecological impacts and economic losses. Bacterial degradation of <em>U. prolifera</em> polysaccharides could accelerate the breakdown of its biomass and transition to the waning phase of green tides. In this study, the strain <em>Alteromonas</em> sp. OM2203 was isolated from seawater samples in the coastal area of Qingdao during a <em>U. prolifera</em> bloom. The genome of strain OM2203 contains one circular chromosome totaling 4,556,409 bp, with a mean GC content of 44.05%. Genomic analysis revealed that <em>Alteromonas</em> sp. OM2203 contains 6 ulvan lyase genes, indicating its potential to degrade <em>U. prolifera</em> polysaccharides and expedite the decomposition of algal biomass. Collectively, the genome of <em>Alteromonas</em> sp. OM2203 provides insights into the role of <em>Alteromonas</em> bacteria in <em>U. prolifera</em> polysaccharide degradation.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101198"},"PeriodicalIF":1.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144070824","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}
Pub Date : 2025-04-16DOI: 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
Astyanax lacustris 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 de novo transcriptome assembly of A. lacustris 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 de novo 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 A. lacustris, enabling future research and molecular studies using this fish species as a model.
Astyanax lacustris 是实验室原生鱼类物种的模型。该物种的繁殖研究已经开展。然而，公共数据库中可获得的基因序列信息相对不足，这阻碍了它们在更全面的研究中的应用，这些研究采用灵敏的分子生物学技术来评估基因表达谱，以鉴定生物标记物。在这篇数据文章中，我们首次报告了从头组装的 A. lacustris 睾丸、卵巢和雄性/雌性垂体的转录组，改进了该鱼种现有的基因序列数据和雄性肝脏的转录组。Illumina 测序产生了 808,023,356 个原始读数，筛选出 752,739,866 个高质量读数。最初，对从头组装进行了过滤，只包括每个组织样本中的蛋白质编码元素，然后合并成最终的泛转录组（PAN），其中包含 109,232 个等位基因。在 EnTAP 的帮助下，根据定制的翼手目蛋白质数据集和 EggNOG 术语对泛转录组进行了功能注释，检索到所有转录本中约 90% 的同源性查询。因此，在这项研究中，我们提供了一个 PAN 和一个定制的 blast 工具，可帮助发现 A. lacustris 新陈代谢通路及其相关基因的基因组信息，从而有助于未来以该鱼种为模型开展研究和分子研究。
{"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}
Pub Date : 2025-02-18DOI: 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
The genus Notacanthus comprises worldwide distributed bathypelagic deep-sea fish species. Despite several interesting ecological traits and their interesting phylogenetic position as relatives of eels, no transcriptomic, genomic, or proteomic resources are currently available. Here, we present a brain and eye transcriptome for two different notacanthid species: the shortfin spiny eel Notacanthus bonaparte (Risso, 1840) and N. arrontei (Bañón et al., 2024). Functional annotation of the transcripts is also provided. These novel datasets will be valuable for future studies on notacanthid fish and the deep-sea bathypelagic fish community.
该属包括分布在世界各地的深海鱼类。尽管有一些有趣的生态特征和它们作为鳗鱼亲戚的有趣的系统发育位置，但目前没有转录组学，基因组学或蛋白质组学资源。在这里，我们展示了两种不同的Notacanthus物种的大脑和眼睛转录组：短鳍刺鳝Notacanthus bonaparte （Risso, 1840）和N. arrontei （Bañón et al., 2024）。还提供了转录本的功能注释。这些新数据集将为今后对深海深海深海鱼类群落的研究提供有价值的数据。
{"title":"A “light in the darkness”: First transcriptomic data from deep-sea spiny eels (Notacanthus, Notacanthiformes)","authors":"André Gomes-dos-Santos , André M. Machado , Francisco Baldó , Juan Carlos Arronte , L. Filipe C. Castro , David Barros-García","doi":"10.1016/j.margen.2025.101182","DOIUrl":"10.1016/j.margen.2025.101182","url":null,"abstract":"<div><div>The genus <em>Notacanthus</em> comprises worldwide distributed bathypelagic deep-sea fish species. Despite several interesting ecological traits and their interesting phylogenetic position as relatives of eels, no transcriptomic, genomic, or proteomic resources are currently available. Here, we present a brain and eye transcriptome for two different notacanthid species: the shortfin spiny eel <em>Notacanthus bonaparte</em> (Risso, 1840) and <em>N. arrontei</em> (<span><span>Bañón et al., 2024</span></span>). Functional annotation of the transcripts is also provided. These novel datasets will be valuable for future studies on notacanthid fish and the deep-sea bathypelagic fish community.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101182"},"PeriodicalIF":1.3,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-12DOI: 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
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 Vibrio 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 bccT and acryloy-CoA reductase gene acuI, which is essential in DMSP cleavage, are identified in the genome of Vibrio sp. D3. Potential DMSP demethylase gene dmdA (26.07 %, amino acid sequence identity) and DMSP lyase gene dddX (26.32 %, amino acid sequence identity) are predicted in the genome of strain D3, whose functions need further experimental verification. Vibrio sp. D3 also contains L-Met gamma-lyase (MegL) to generate MeSH from L-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.
{"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}
Pub Date : 2025-02-12DOI: 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
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. Vreelandella piezotolerans 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 Vreelandella genus, and provides a crucial foundation for further investigation of D-amino acids metabolism.
d -氨基酸通常被认为是只存在于细菌中的独特代谢物。它们不仅能修饰细菌细胞壁，促进植物生长，还能参与哺乳动物的免疫调节，在自然界中具有重要意义。从黄海沿岸海水中分离出一种革兰氏阴性好氧细菌——压耐受性V23。本文报道了菌株V23的基因组及其利用d -氨基酸的基因组特征。菌株V23基因组由一条单圆形染色体组成，全长3,926,051 bp， GC含量为58.11%。基因组分析表明，菌株V23具有多种与d -氨基酸代谢有关的基因和一条d -氨基酸合成肽聚糖的途径。结果表明，菌株V23具有利用d -氨基酸的能力。菌株V23已被证实能够以不同的d -氨基酸作为唯一的氮源生长。本研究也为进一步了解Vreelandella属菌株的生理代谢特性和种间多样性，为进一步研究d -氨基酸代谢提供了重要的基础。
{"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}
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