Marine genomics最新文献_第3页

The complete genome sequence of proteases-producing Shewanella sp. H8 isolated from Antarctica 从南极洲分离的产蛋白酶的雪旺氏菌 H8 的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101147

Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang

{"title":"The complete genome sequence of proteases-producing Shewanella sp. H8 isolated from Antarctica","authors":"Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang","doi":"10.1016/j.margen.2024.101147","DOIUrl":"10.1016/j.margen.2024.101147","url":null,"abstract":"<div><div>Bacteria of the genus Shewanella in the class Gammaproteobacteria are widely distributed in marine environments. Shewanella sp. H8, was isolated from a red algae sample collected from Nelson Island, Antarctica. Here, we present the complete genome sequence of strain H8, which consists of a single circular chromosome comprising 4,490,743 nucleotides with 40.59 % G + C content without any plasmid. In total, 3983 protein coding genes, 95 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain H8 showed that it contains four cold shock proteins and three fatty acid desaturases and possesses the potential to synthesize hglE-KS, arylpolyene, betalactone and RiPP-like compounds. Through genomic annotation, 91 protease-encoding genes were identified within the genome of strain H8. These proteases are classified into six categories based on their catalytic types. Among these proteases, metalloproteinases and serine proteases are dominant. These proteases may provide carbon and nitrogen sources to H8 by degrading proteins in the environment. This study will provide potential genetic information for the future research and development of cold-adapted proteases.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"78 ","pages":"Article 101147"},"PeriodicalIF":1.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142416810","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 analysis of deep-sea hydrothermal sulfur-oxidizing bacterium Sulfitobacter sp. TCYB15 associated with mussel Bathymodiolus marisindicus and insights into its habitat adaptation 与贻贝Bathymodiolus marisindicus相关的深海热液硫氧化细菌Sulfitobacter sp.

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101148

Yadan Deng , Yunjin Zhu , Jiaxuan He , Xin Yin , Qian Li , Zhengxing Chen , Bingshu Wang , Li Zheng

引用次数: 0

The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin 可产生抗真菌抗生素 Scopafungin 的海洋放线菌--链霉菌 FIM 95-F1 的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-09-06 DOI: 10.1016/j.margen.2024.101146

Peng Fei , Lin Yangjun , Zhuang Yuee , Lin Ping , Liu Chengzhi , Chen Linlin , Jiang Hong , Lian Yunyang , Zhang Wenzhou , Huang Youxia

{"title":"The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin","authors":"Peng Fei , Lin Yangjun , Zhuang Yuee , Lin Ping , Liu Chengzhi , Chen Linlin , Jiang Hong , Lian Yunyang , Zhang Wenzhou , Huang Youxia","doi":"10.1016/j.margen.2024.101146","DOIUrl":"10.1016/j.margen.2024.101146","url":null,"abstract":"<div>Streptomyces FIM95-F1, an actinomycete originating from mangroves of Quanzhou bay, exhibits the capability to produce the antifungal antibiotic scopafungin. Here, the complete genome of Streptomyces sp. FIM95-F1 is presented with a GC content of 71.04 %, comprising a 9,718,239-bp linear chromosome, 8236 protein-coding genes, 18 rRNA genes, 64 tRNA genes, 2 prophages, and 58 CRISPR regions. In silico analysis revealed the presence of 42 biosynthetic gene clusters (BGCs), the majority of which demonstrated similarity to both known and novel BGCs responsible for the biosynthesis of previously known and novel bioactive agents of microbial origin. A comprehensive comparison between the scopafungin BGC and niphimycin BGC has indicated a potential shared pathway for the biosynthesis of scopafungin. One of the intriguing findings of this study was the discovery of at least two novel BGCs (namely Cluster 26 and Cluster 32) present within biosynthetic gene clusters. Our findings suggest that Streptomyces sp. FIM95-F1 possesses significant potential in producing a diverse array of both known and novel bioactive compounds, which could be valuable in the field of drug discovery.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"78 ","pages":"Article 101146"},"PeriodicalIF":1.3,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147689","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 Rhodopirellula sp. P2 reveals its role in fucoidan degradation Rhodopirellula sp. P2 的基因组分析揭示了其在褐藻糖胶降解中的作用

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-08-29 DOI: 10.1016/j.margen.2024.101145

Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang

{"title":"Genomic analysis of Rhodopirellula sp. P2 reveals its role in fucoidan degradation","authors":"Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang","doi":"10.1016/j.margen.2024.101145","DOIUrl":"10.1016/j.margen.2024.101145","url":null,"abstract":"<div>Fucoidan, the main polysaccharide in various species of brown seaweed, has a high annual production. It is an important source of marine organic carbon and exhibits diverse biological activities and significant application potential. Rhodopirellula sp. P2, a novel marine bacterium of the phylum Planctomycetota, was isolated from intertidal algae samples collected from the Weihai coast, the Yellow Sea, China. The strain P2 is a Gram-negative, aerobic, and pear-shaped bacterium. Here, we report the complete genome sequence of Rhodopirellula sp. P2. The genome of strain P2 consists of a single circular chromosome with 7,291,416 bp and a GC content of 57.38 %, including 5462 protein-coding genes, 2 rRNA genes, and 48 tRNA genes. Genomic analysis revealed that strain P2 possessed 173 CAZymes and 106 sulfatases, indicating that strain P2 has the potential ability to utilize multiple polysaccharides, especially hydrolyze fucoidan to fucose. The genome of strain P2 also encodes a gene cluster related to bacterial microcompartment, suggesting the ability of strain P2 to metabolize fucose. These results enhance the understanding of the diversity and ecological functions of Planctomycetota, and also facilitate the exploitation of Planctomycetota and enzyme resources to utilize fucoidan. This study provides genetic insights into fucoidan catabolism by Planctomycetota, expanding our understanding of fucoidan-degrading microbial groups.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"78 ","pages":"Article 101145"},"PeriodicalIF":1.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096649","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 the 4-hydroxybenzoate-degrading bacterium Gymnodinialimonas sp. 57CJ19, a potential novel species from intertidal sediments 潮间带沉积物中的潜在新物种--4-羟基苯甲酸盐降解细菌Gymnodinialimonas sp.57CJ19的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-07-17 DOI: 10.1016/j.margen.2024.101135

Dong-Hui Li , Ning Zheng , Zhen-Hai Liu , Xiao-Rui Dong , Chen Zhao , Shi-Gan Yan , Bin-Bin Xie

引用次数: 0

The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation 含有丰富多糖降解基因的平面菌P1的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101126

Jia-Xuan Wang, Jing Wang, Ji-Qing Liu, Jian Li, Wen-Xin Jiang, Fei Xu, Ping-Yi Li, Qi-Long Qin, Xiu-Lan Chen, Xi-Ying Zhang

{"title":"The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation","authors":"Jia-Xuan Wang, Jing Wang, Ji-Qing Liu, Jian Li, Wen-Xin Jiang, Fei Xu, Ping-Yi Li, Qi-Long Qin, Xiu-Lan Chen, Xi-Ying Zhang","doi":"10.1016/j.margen.2024.101126","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101126","url":null,"abstract":"<div>Isolated from intertidal sediment of the Yellow Sea, China, Bremerella sp. P1 putatively represents a novel species within the genus Bremerella of the family Pirellulaceae in the phylum Planctomycetota. The complete genome of strain P1 comprises a single circular chromosome with a size of 6,955,728 bp and a GC content of 55.26%. The genome contains 5772 protein-coding genes, 80 tRNA and 6 rRNA genes. A total of 147 CAZymes and 128 sulfatases have been identified from the genome of strain P1, indicating that the strain has the capability to degrade a wide range of polysaccharides. Moreover, a gene cluster related to bacterial microcompartments (BMCs) formation containing genes encoding the shell proteins and related enzymes to metabolize fucose or rhamnose is also found in the genome of strain P1. The genome of strain P1 represents the second complete one in the genus Bremerella, expanding the understanding of the physiological and metabolic characteristics, interspecies diversity, and ecological functions of the genus.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101126"},"PeriodicalIF":1.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434258","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

Marine eDNA sampling from submerged surfaces with paint rollers 用油漆辊从水下表面采集海洋 eDNA 样本

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101127

Simon Jarman , Jason B. Alexander , Kathryn L. Dawkins , Sherralee S. Lukehurst , Georgia M. Nester , Shaun Wilkinson , Michael J. Marnane , Justin I. McDonald , Travis S. Elsdon , Euan S. Harvey

{"title":"Marine eDNA sampling from submerged surfaces with paint rollers","authors":"Simon Jarman , Jason B. Alexander , Kathryn L. Dawkins , Sherralee S. Lukehurst , Georgia M. Nester , Shaun Wilkinson , Michael J. Marnane , Justin I. McDonald , Travis S. Elsdon , Euan S. Harvey","doi":"10.1016/j.margen.2024.101127","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101127","url":null,"abstract":"<div>Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101127"},"PeriodicalIF":1.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434767","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

Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China 从中国南海沉积物中分离的深海细菌 Salinimicrobium sp.

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-06-18 DOI: 10.1016/j.margen.2024.101125

Shijie Bai , Kun Shang , Shuqian Zeng , Ziming Huang , Zhuang Han

{"title":"Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China","authors":"Shijie Bai , Kun Shang , Shuqian Zeng , Ziming Huang , Zhuang Han","doi":"10.1016/j.margen.2024.101125","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101125","url":null,"abstract":"<div>Salinimicrobium sp. 3283s is an aerobic, golden-yellow pigment-producing, Flavobacteriaceae bacterium isolated from the sediments at the depth of 1751 m in the South China Sea. In this study, we present the complete genome sequence of strain 3283s, which only have a single circular chromosome comprising 3,702,683 bp with 41.41% G + C content and no circular plasmid. In total, 3257 protein coding genes, 45 tRNA, 9 rRNA, and 13 sRNA genes were obtained. In terms of the function of gene annotation, strain 3283s was more different from Salinimicrobium oceani J15B91, which was isolated from the South China Sea at a similar depth, and more similar to a Mariana Trench-derived strain Salinimicrobium profundisediminis MT39, which was closer in phylogenetic taxonomic status, suggesting that strain 3283s possesses a stronger potential to adapt to the deep-sea environment. Furthermore, the high- pressure simulations also confirmed that strain 3283s can grow in both 30 MPa and 60 MPa hydrostatic pressure environments, and that it grows better in 30 MPa hydrostatic pressure environments than in 60 MPa hydrostatic pressure environments. In addition, we found a large number of genes in strain 3283s that can promote better adaptation of the bacteria to the low oxygen and high hydrostatic pressure (HHP) environment of the deep sea, such as biosynthetic enzymes of antioxidant pigments, genes encoding cytochromes with enhanced affinity for oxygen, proteins for adaptation to HHP, and genes encoding TonB-dependent transporters in the absence of flagella.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101125"},"PeriodicalIF":1.9,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141423706","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 profiling of biosynthetic potentials of medicinal secondary metabolites for ‘Aliisedimentitalea scapharcae’ KCTC 42119T, isolated from ark shell 从蚶壳中分离出的'Aliisedimentitalea scapharcae' KCTC 42119T 的药用次生代谢物生物合成潜力基因组剖析

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-06-07 DOI: 10.1016/j.margen.2024.101124

Jin-Cheng Rong , Lin-Lin Cui , Na Li , Mao-Li Yi , Bo-Tao Huang , Qi Zhao

{"title":"Genomic profiling of biosynthetic potentials of medicinal secondary metabolites for ‘Aliisedimentitalea scapharcae’ KCTC 42119T, isolated from ark shell","authors":"Jin-Cheng Rong , Lin-Lin Cui , Na Li , Mao-Li Yi , Bo-Tao Huang , Qi Zhao","doi":"10.1016/j.margen.2024.101124","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101124","url":null,"abstract":"<div>Microorganisms living with higher organisms are valuable sources of bioactive substances like antibiotics, which could assist them competing for more and better nutrients or space. Here, we focused on a marine animal-associated bacterium, ‘Aliisedimentitalea scapharcae’ KCTC 42119T, which was isolated from ark shell collected from Gang-Jin bay of South Korea. We evaluated its biosynthetic potentials of medicinal secondary metabolites by de novo genome sequencing. The complete genome of strain KCTC 42119T sequenced is 5,083,900 bp and is comprised of one circular chromosome and four circular plasmids. Functional genome analysis by antiSMASH v7.1.0 showed that there are nine biosynthetic gene clusters encoded on the chromosome. The annotated secondary metabolites include antibiotic corynecin, cytoprotective ectoine and antineoplastic ET-743 (Yondelis), which suggested strain KCTC 42119T possesses potentials to synthesize a series of secondary metabolites of pharmaceutical utility. Genome analysis of ‘A. scapharcae’ also provides more insights into mining bioactive substances from animal-associated microorganisms.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101124"},"PeriodicalIF":1.9,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141289753","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 Kushneria phosphatilytica YCWA18T reveals the P-solubilizing activity of the genus Kushneria Kushneria phosphatilytica YCWA18T 的完整基因组序列揭示了 Kushneria 属的溶解 P 活性

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-05-30 DOI: 10.1016/j.margen.2024.101123

Guang-xun Du , Wen-sheng Yu , Ji-kun Su , Guo-chong Liu , Ping Gao , Xu-guang Hong , Ling-yun Qu

{"title":"Complete genome sequence of Kushneria phosphatilytica YCWA18T reveals the P-solubilizing activity of the genus Kushneria","authors":"Guang-xun Du , Wen-sheng Yu , Ji-kun Su , Guo-chong Liu , Ping Gao , Xu-guang Hong , Ling-yun Qu","doi":"10.1016/j.margen.2024.101123","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101123","url":null,"abstract":"<div>Kushneria phosphatilytica YCWA18T (= CGMCC 1.9149T = NCCB 100306T) was isolated from sediment collected in a saltern on the eastern coast of Yellow Sea in China. The genome was sequenced and comprised of one circular chromosome with the size of 3,624,619 bp and DNA G + C content of 59.13%. A total of 3267 protein-coding genes, 64 tRNA genes and 12 rRNA genes were obtained. Genomic annotation indicated that the genome of K. phosphatilytica YCWA18T had 34 genes involved in phosphorus (P) solubilization/metabolism, e.g., gdh, pqq, phoA, phoD and phoX, which products can convert insoluble P-containing compounds to more bio-available dissolved inorganic P. Comparative genomic analysis of Kushneria strains revealed that gdh, pqq, phoA, phoD and phoX were widely distributed in these strains, indicating the genus Kushneria may play an important role in the P cycle. Additionally, a multitude of salt tolerance genes were detected in the genome of K. phosphatilytica YCWA18T. This study and the genome sequence data will be available for further research and will provide insights into potential biotechnological and agricultural applications of Kushneria strains.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101123"},"PeriodicalIF":1.9,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240375","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