Marine genomics最新文献_第4页

Complete genome sequence of a novel Pseudomonas sp. IT1137 isolated from Antarctic intertidal sediment showing potential for alkane degradation at low temperatures 从南极潮间带沉积物中分离出的新型假单胞菌 IT1137 的完整基因组序列显示其在低温下降解烷烃的潜力

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-05-14 DOI: 10.1016/j.margen.2024.101122

Hui-Yan Ge , Yi-He Zhang , Yong-Qiang Hu , Wei Han , Yu Du , Ting Hu , Yin-Xin Zeng

{"title":"Complete genome sequence of a novel Pseudomonas sp. IT1137 isolated from Antarctic intertidal sediment showing potential for alkane degradation at low temperatures","authors":"Hui-Yan Ge , Yi-He Zhang , Yong-Qiang Hu , Wei Han , Yu Du , Ting Hu , Yin-Xin Zeng","doi":"10.1016/j.margen.2024.101122","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101122","url":null,"abstract":"<div>Pseudomonas species are known for their diverse metabolic abilities and broad ecological distribution. They are fundamental components of bacterial communities and perform essential ecological functions in the environment. A psychrotrophic Pseudomonas sp. IT1137 was isolated from intertidal sediment in the coastal region of the Fildes Peninsula, King George Island, Antarctica. The strain contained a circular chromosome of 5,346,697 bp with a G + C content of 61.66 mol% and one plasmid of 4481 bp with a G + C content of 64.61 mol%. A total of 4848 protein-coding genes, 65 tRNA genes and 15 rRNA genes were obtained. Genome sequence analysis revealed that strain IT1137 not only is a potentially novel species of the genus Pseudomonas but also harbors functional genes related to nitrogen, sulfur and phosphorus cycling. In addition, genes involved in alkane degradation, ectoine synthesis and cyclic lipopeptide (CLP) production were detected in the bacterial genome. The results indicate the potential of the strain Pseudomonas sp. IT1137 for biotechnological applications such as bioremediation and secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold coastal environments.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101122"},"PeriodicalIF":1.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140918691","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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Complete genome sequence analysis of a biosurfactant-producing bacterium Bacillus velezensis L2D39 生物表面活性剂生产细菌 Bacillus velezensis L2D39 的全基因组序列分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-05-07 DOI: 10.1016/j.margen.2024.101113

Yihan Ding , Shiping Wei , Gaiyun Zhang

{"title":"Complete genome sequence analysis of a biosurfactant-producing bacterium Bacillus velezensis L2D39","authors":"Yihan Ding , Shiping Wei , Gaiyun Zhang","doi":"10.1016/j.margen.2024.101113","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101113","url":null,"abstract":"<div>Biosurfactants are amphipathic molecules with high industrial values owing to their chemical properties and stability under several environmental conditions. They have become attractive microbial products in the emerging biotechnology industry, offering a potential environmentally-friendly alternative to synthetic surfactants. Nowadays, several types of biosurfactants are commercially available for a wide range of applications in healthcare, agriculture, oil extraction and environmental remediation. In this study, a marine bacterium Bacillus velezensis L2D39 with the capability of producing biosurfactants was successfully isolated and characterized. The complete genome sequence of the bacterium B. velezensis L2D39 was obtained using PacBio Sequel HGAP.4, resulting in a sequence consisting of 4,140,042 base pairs with a 46.2 mol% G + C content and containing 4071 protein-coding genes. The presence of gene clusters associated with biosurfactants was confirmed through antiSMASH detection. The analysis of complete genome sequence will provide insight into the potential applications of this bacterium in biotechnological and natural product biosynthesis.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101113"},"PeriodicalIF":1.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140879644","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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Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling 从马里亚纳海沟分离的 Alteromonas sp.

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-05-07 DOI: 10.1016/j.margen.2024.101112

Yue Lin , Min Zhang , Yu-Xiang Lai , Teng Liu , Meng Meng , Yan Sun , Yu Wang , Qing-Yu Dong , Chen-Xi Li , Meng-Xue Yu , Jin Cheng , Shu-Jun Liu , Xuan Shao , Nan Zhang , Chun-Yang Li

{"title":"Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling","authors":"Yue Lin , Min Zhang , Yu-Xiang Lai , Teng Liu , Meng Meng , Yan Sun , Yu Wang , Qing-Yu Dong , Chen-Xi Li , Meng-Xue Yu , Jin Cheng , Shu-Jun Liu , Xuan Shao , Nan Zhang , Chun-Yang Li","doi":"10.1016/j.margen.2024.101112","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101112","url":null,"abstract":"<div>Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in stress tolerance, global carbon and sulfur cycling, and chemotaxis. It is the main precursor of the climate active gas dimethyl sulfide (DMS), which is the greatest natural source of bio‑sulfur transferred from ocean to atmosphere. Alteromonas sp. M12, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench at the depth of 2500 m. Here, we report the complete genome sequence of strain M12 and its genomic characteristics to import and utilize DMSP. The genome of strain M12 contains one circular chromosome (5,012,782 bp) with the GC content of 40.88%. Alteromonas sp. M12 can grow with DMSP as a sole carbon source, and produced DMS with DMSP as a precursor. Genomic analysis showed that strain M12 contained a set of genes involved in the downstream steps of DMSP cleavage, but no known genes encoding DMSP transporters or DMSP lyases. The results indicated that this strain contained novel DMSP transport and cleavage genes in its genome which warrants further investigation. The import of DMSP into cells may be a strategy of strain M12 to adapt the hydrostatic pressure environment in the Mariana Trench, as DMSP can be used as a hydrostatic pressure protectant. This study sheds light on the catabolism of DMSP by deep-sea bacteria.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"76 ","pages":"Article 101112"},"PeriodicalIF":1.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140879643","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 sequencing of Hortaea werneckii M-3 for identifying polyester polyurethane degrading enzymes 对 Hortaea werneckii M-3 进行全基因组测序以确定聚酯聚氨酯降解酶

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-05-02 DOI: 10.1016/j.margen.2024.101111

Minghuang Ling , Kai Zhang , Juan Hu , Xiaomei Huang , Gaili Fan , Hans-Peter Grossart , Zhuhua Luo

引用次数: 0

Genomic characteristics of nine Nitrospirota metagenome-assembled genomes in deep-sea sediments from East Pacific polymetallic nodules zone 东太平洋多金属结核区深海沉积物中九个硝螺菌元基因组的基因组特征

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-03-22 DOI: 10.1016/j.margen.2024.101107

Zhi-Hao Ding , Yue-Hong Wu

{"title":"Genomic characteristics of nine Nitrospirota metagenome-assembled genomes in deep-sea sediments from East Pacific polymetallic nodules zone","authors":"Zhi-Hao Ding , Yue-Hong Wu","doi":"10.1016/j.margen.2024.101107","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101107","url":null,"abstract":"<div>Previously studies have reported that MAGs (Metagenome-assembled genomes) belong to “Candidatus Manganitrophaceae” of phylum Nitrospirota with chemolithoautotrophic manganese oxidation potential exist in freshwater and hydrothermal environments. However, Nitrospirota members with chemolithoautotrophic manganese oxidation potential have not been reported in other marine environments. Through metagenomic sequencing, assembly and binning, nine metagenome-assembled genomes belonging to Nitrospirota are recovered from sediment of different depths in the polymetallic nodule area. Through the key functional genes annotation results, we find that these Nitrospirota have limited potential to oxidize organic carbon because of incomplete tricarboxylic acid cycle and most of them (6/9) have carbon dioxide fixation potential through different pathway (rTCA, WL or CBB). One MAG belongs to order Nitrospirales has the potential to use manganese oxidation to obtain energy for carbon fixation. In addition to manganese ions, the oxidation of inorganic nitrogen, sulfur, hydrogen and carbon monoxide may also provide energy for the growth of these Nitrospirota. In addition, different metal ion transport systems can help those Nitrospirota to resist heavy metal in sediment. Our work expands the understanding of the metabolic potential of Nitrospirota in sediment of polymetallic nodule region and may contributes to promoting the study of chemolithoautotrophic manganese oxidation.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"75 ","pages":"Article 101107"},"PeriodicalIF":1.9,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140187658","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

An historical “wreck”: A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978 历史上的 "沉船"：海军船虫 Teredo navalis Linnaeus 的转录组组装，1978 年

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-02-27 DOI: 10.1016/j.margen.2024.101097

André Gomes-dos-Santos , Marcos Domingues , Raquel Ruivo , Elza Fonseca , Elsa Froufe , Diana Deyanova , João N. Franco , L. Filipe C. Castro

{"title":"An historical “wreck”: A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978","authors":"André Gomes-dos-Santos , Marcos Domingues , Raquel Ruivo , Elza Fonseca , Elsa Froufe , Diana Deyanova , João N. Franco , L. Filipe C. Castro","doi":"10.1016/j.margen.2024.101097","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101097","url":null,"abstract":"<div>Historically famous for their negative impact on human-built marine wood structures, mollusc shipworms play a central ecological role in marine ecosystems. Their association with bacterial symbionts, providing cellulolytic and nitrogen-fixing activities, underscores their exceptional wood-eating and wood-boring behaviours, improving energy transfer and the recycling of essential nutrients locked in the wood cellulose. Importantly, from a molecular standpoint, a minute of omic resources are available from this lineage of Bivalvia. Here, we produced and assembled a transcriptome from the globally distributed naval shipworm, Teredo navalis (family Teredinidae). The transcriptome was obtained by sequencing the total RNA from five equidistant segments of the whole body of a T. navalis specimen. The quality of the produced assembly was accessed with several statistics, revealing a highly contiguous (1194 N50) and complete (over 90% BUSCO scores for Eukaryote and Metazoan databases) transcriptome, with nearly 38,000 predicted ORF, more than half being functionally annotated. Our findings pave the way to investigate the unique evolutionary biology of these highly modified bivalves and lay the foundation for an adequate gene annotation of a full genome sequence of the species.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"74 ","pages":"Article 101097"},"PeriodicalIF":1.9,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139986022","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 analysis of Bacillus velezensis A5, a promising biocontrol agent from the Pacific Ocean 来自太平洋的一种很有前途的生物控制剂--Bacillus velezensis A5 的全基因组序列分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-02-01 DOI: 10.1016/j.margen.2024.101087

Shunhua Ji , Yin Tian , Guangxin Xu , Yiqiang Chen , Jingjing Li , Teng Long , Wei He , Jianqiang Fan , Xixiang Tang

引用次数: 0

Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella) 原雌性变性鱼类哈氏沙鲅（Parapercis pulchella）的参考转录组汇编

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-02-01 DOI: 10.1016/j.margen.2024.101086

Akifumi Yao, Hisanori Kohtsuka, Toru Miura

{"title":"Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella)","authors":"Akifumi Yao, Hisanori Kohtsuka, Toru Miura","doi":"10.1016/j.margen.2024.101086","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101086","url":null,"abstract":"<div>The harlequin sandsmelt (Parapercis pulchella) is a female-to-male sex change fish in which functional females possess ovotestes that consist of both ovarian and testicular tissues. These features indicate that this species could be an excellent model for studying the flexibility of sex differentiation in vertebrates. However, genetic resources in this species have so far been limited. Therefore, in this study, the reference transcriptome of this fish was constructed through RNA-sequencing, de novo transcriptome assembly, superTranscripts construction, and functional annotations. To obtain as many genes as possible, RNA was extracted from various tissues (brains, gills, hearts, livers, guts, and gonads) and various sexual stages (females, individuals during sex change, and males) and then subjected to sequencing and downstream analyses. As a result, 91,884 representative transcripts with 32,627 protein-coding sequences were generated. 72.2% of protein-coding sequences (23,566 sequences) were functionally annotated. Also, our analysis shows that the superTranscripts method effectively removes redundant sequences from raw-assembled data compared with other strategies. The resultant dataset is a valuable resource for future molecular developmental studies on sex change in P. pulchella.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"73 ","pages":"Article 101086"},"PeriodicalIF":1.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675043","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 whole-body transcriptome assembly of the annelid worm Hediste diversicolor 环带蠕虫 Hediste diversicolor 的全身转录组汇编

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-01-12 DOI: 10.1016/j.margen.2024.101084

André M. Machado , Rodrigo Samico , Marcos Domingues , Andreas Hagemann , Luísa M.P. Valente , Arne M. Malzahn , André Gomes-dos-Santos , Raquel Ruivo , Juan Carlos Navarro , Óscar Monroig , L. Filipe C. Castro

{"title":"A whole-body transcriptome assembly of the annelid worm Hediste diversicolor","authors":"André M. Machado , Rodrigo Samico , Marcos Domingues , Andreas Hagemann , Luísa M.P. Valente , Arne M. Malzahn , André Gomes-dos-Santos , Raquel Ruivo , Juan Carlos Navarro , Óscar Monroig , L. Filipe C. Castro","doi":"10.1016/j.margen.2024.101084","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101084","url":null,"abstract":"<div>The Annelida phylum is composed of a myriad of species exhibiting key phenotypic adaptations. They occupy key ecological niches in a variety of marine, freshwater and terrestrial ecosystems. Importantly, the increment of omic resources is rapidly modifying the taxonomic landscape and knowledge of species belonging to this phylum. Here, we comprehensively characterised and annotated a transcriptome of the common ragworm, Hediste diversicolor (OF Müller). This species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, H. diversicolor plays an important role in benthic food webs. Given its commercial value, H. diversicolor is a promising candidate for aquaculture development and production in farming facilities, under a circular economy framework. We used Illumina next-generation sequencing technology, to produce a total of 105 million (M) paired-end (PE) raw reads and generate the first whole-body transcriptome assembly of H. diversicolor species. This high-quality transcriptome contains 69,335 transcripts with an N50 transcript length of 2313 bp and achieved a BUSCO gene completeness of 97.7% and 96% in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological applications using this species.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"74 ","pages":"Article 101084"},"PeriodicalIF":1.9,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139433409","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 Psychrobacter cibarius AOSW16051, a trimeric autotransporter adhesin synthesizing bacterium isolated from the Baltic Sea 从波罗的海分离的三聚体自转运粘附素合成细菌 Cibarius AOSW16051 的完整基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-12-14 DOI: 10.1016/j.margen.2023.101082

Xiao-Yu Wang , Tianyin Miao , Yuyi Wang , Zhangwei Guo , Jin-Long Yang , Xiao Liang

{"title":"Complete genome sequence of Psychrobacter cibarius AOSW16051, a trimeric autotransporter adhesin synthesizing bacterium isolated from the Baltic Sea","authors":"Xiao-Yu Wang , Tianyin Miao , Yuyi Wang , Zhangwei Guo , Jin-Long Yang , Xiao Liang","doi":"10.1016/j.margen.2023.101082","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101082","url":null,"abstract":"<div>Bacteria of the genus Psychrobacter are widely distributed in the global low-temperature marine environment and have been studied for their effects on the settlement and metamorphosis of marine invertebrates. Psychrobacter cibarius AOSW16051 was isolated from the surface water samples of the Baltic Sea on the edge of the Arctic Ocean. Here, we present the complete genome of strain AOSW16051, which consists of a circular chromosome composed of 3,425,040 nucleotides with 42.98% G + C content and a circular plasmid composed of 5846 nucleotides with 38.66% G + C content. The genes predicted in this strain showed its strong outer membrane system, type VI secretion system and adhesion system. Trimeric autotransporter adhesins (TAAs) has been identified in the genome of P. cibarius AOSW16051, which has a variety of biological functions in interacting with host cells. However, there are no reports on TAAs in marine bacteria and aquatic pathogenic bacteria. By analyzing the genomic data, we can gain valuable insights to enhance our understanding of the physiological characteristics of P. cibarius, as well as the biological functions of TAAs and their role in triggering metamorphosis of invertebrate larvae.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"74 ","pages":"Article 101082"},"PeriodicalIF":1.9,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138656628","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