Marine genomics最新文献_第10页

De novo transcriptomes for two species of snappers from the Western Atlantic (Lutjanus griseus and Lutjanus synagris) 西大西洋两种鲷鱼(Lutjanus griseus和Lutjanus synagris)的从头转录组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101005

Adam Hallaj , Logan F. Turner , Carolyn A. McArdle, Moisés A. Bernal

引用次数: 0

Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae 海洋玫瑰杆菌系Ruegeria sp. YS9与5个红藻质粒的全基因组序列分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.100997

Qun-Jian Yin , Fang-Chao Zhu , Hong-Zhi Tang , Xu-Yang Chen , Xin Liu , Li-Chang Tang , Xue-Gong Li

{"title":"Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae","authors":"Qun-Jian Yin , Fang-Chao Zhu , Hong-Zhi Tang , Xu-Yang Chen , Xin Liu , Li-Chang Tang , Xue-Gong Li","doi":"10.1016/j.margen.2022.100997","DOIUrl":"10.1016/j.margen.2022.100997","url":null,"abstract":"<div>Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of 4.30 Mb and average GC content of 58.39%. In total, 4129 CDSs, 52 tRNA genes and 9 rRNA genes were obtained. Genomic analysis of strain YS9 revealed that 85 CAZymes were organized in 147 PUL-associated CAZymes involved in polysaccharides metabolism, which were the highest among its two closely related Ruegeria strains. Numerous PULs related to degradation on the cell wall of algae, especially agar, indicated its major player role in the remineralization of algal-derived carbon. Further, the existence of multiple plasmids provided strain YS9 with distinct advantages to facilitate its rapid environmental adaptation, including polysaccharide metabolism, denitrification, resistance to heavy metal stresses such as copper and cobalt, type IV secretion systems and type IV toxin-antitoxin systems, which were obviously different from the two Ruegeria strains. This study provides evidence for polysaccharide metabolic capacity and functions of five plasmids in strain YS9, broadening our understanding of the ecological roles of bacteria in the environment around red algae and the function patterns of plasmids in marine Roseobacter lineage members for environmental adaptation.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"67 ","pages":"Article 100997"},"PeriodicalIF":1.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10581017","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

Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4 红海裸鳃诺卡藻相关细菌的生物活性及dassonvilnocardiopsis RACA-4全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101004

Hossam H. Elfeky , Amro Hanora , Samar M. Solyman

{"title":"Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4","authors":"Hossam H. Elfeky , Amro Hanora , Samar M. Solyman","doi":"10.1016/j.margen.2022.101004","DOIUrl":"10.1016/j.margen.2022.101004","url":null,"abstract":"<div>Microorganisms associated with marine invertebrates consider an important source of bioactive products. This study aimed to screen for antimicrobial and anticancer activity of crude extracts of bacteria associated with Red sea nudibranchs and molecular identification of the bioactive isolates using 16Sr RNA sequencing, in addition to whole-genome sequencing of one of the most bioactive bacteria. This study showed that bacteria associated with Red sea nudibranchs are highly bioactive and 16Sr RNA sequencing results showed that two isolates belonged to Firmicutes, and two isolates belonged to Proteobacteria, and Actinobacteria. The whole genome sequence data of the isolated Nocardiopsis RACA4 isolate has an estimated genome length of 6,721,839 bp and the taxonomy showed it belongs to the bacteria Nocardiopsis dassonvillei. The De novo assembly of RACA-4 paired reads using Unicycler v0.4.8 initially yielded 97 contigs with an N50 value of 214,568 bp and L50 value of 10, The resulting assembly was further mapped to the reference genome Nocardiopsis dassonvillei strain NCTC10488 using RagTag software v.2.1.0 and a final genome assembly resulted in 39 contigs and N50 value of 6,726,007 and L50 of 1. Genome mining using anti-smash showed around 9.1% of the genome occupied with genes related to secondary metabolites biosynthesis. A wide variety of secondary metabolites belonging to Polyketides, Terpenes, and nonribosomal peptides were predicted with high degree of similarity to known compounds. Non-characterized clusters were also found which suggest new natural compounds discovered by further studies.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"67 ","pages":"Article 101004"},"PeriodicalIF":1.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10627920","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: 4

De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress 濒危海草斑纹藻转录组的从头组装和注释:来自热胁迫下差异基因表达的见解

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-12-01 DOI: 10.1016/j.margen.2022.100984

Andrew Ndhlovu, Sophie von der Heyden

{"title":"De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress","authors":"Andrew Ndhlovu, Sophie von der Heyden","doi":"10.1016/j.margen.2022.100984","DOIUrl":"10.1016/j.margen.2022.100984","url":null,"abstract":"<div>Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of how pressures such as climate change affect foundational species, including Z. capensis are crucial to supporting their conservation and underpin restoration efforts. Here we use ecological transcriptomics to study key functional responses of Z. capensis through quantification of gene expression after thermal stress and present the first reference transcriptome of Z. capensis. Four de novo reference assemblies (Trinity, IDBA-tran, RNAspades, SOAPdenovo) filtered through the EvidentialGene pipeline resulted in 153,755 transcripts with a BUSCO score of 66.1% for completeness. Differential expression analysis between heat stressed (32 °C for three days) and pre-warming plants identified genes involved in photosynthesis, oxidative stress, translation, metabolic and biosynthetic processes in the Z. capensis thermal stress response. This reference transcriptome is a significant contribution to the limited available genomic resources for Z. capensis and represents a vital tool for addressing questions around the species restoration and potential functional responses to warming marine environments.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"66 ","pages":"Article 100984"},"PeriodicalIF":1.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40363071","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: 1

Complete genome sequence of piezotolerant Stutzerimonas kunmingensis 7850S isolated from the sediment of the Mariana Trench 从马里亚纳海沟沉积物中分离出的耐压性kunmingstutzerimensis 7850S的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-12-01 DOI: 10.1016/j.margen.2022.100996

Jia-Wei Wang , Kun Shang , Sheng-Yi Wu , Bo-Yu Zhu , Mei-Gui Han , Yuan Zhao , Yi-Qiu Chen , Jia Xie , Bo Huang , Zhuang Han

{"title":"Complete genome sequence of piezotolerant Stutzerimonas kunmingensis 7850S isolated from the sediment of the Mariana Trench","authors":"Jia-Wei Wang , Kun Shang , Sheng-Yi Wu , Bo-Yu Zhu , Mei-Gui Han , Yuan Zhao , Yi-Qiu Chen , Jia Xie , Bo Huang , Zhuang Han","doi":"10.1016/j.margen.2022.100996","DOIUrl":"10.1016/j.margen.2022.100996","url":null,"abstract":"<div>Stutzerimonas kunmingensis 7850S is a piezotolerant bacterium isolated from the sediment of the Mariana trench. Here, we described the complete genome of strain 7850S, which contains a single circular chromosome of 4,775,870 base pairs with 62.66% G + C content, and harbors 4494 protein-coding genes, 65 transfer RNA genes, and 12 ribosomal RNA genes. The experimental results showed that strain 7850S could grow under hydrostatic pressure of 0.1–70 MPa. Genomic analyses led to identifications of numbers of high hydrostatic pressure-associated genes, such as the ones associated with unsaturated fatty acids, betaine, and ectoine. A complete set of denitrification genes and some heavy metal detoxification genes were also found in this strain. The presence of these genes suggests metabolic characteristics for adaption to hadal environments and provides insights to further understand adaption strategies and ecological roles of Stutzerimonas in hadal environments.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"66 ","pages":"Article 100996"},"PeriodicalIF":1.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40696158","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 denitrifying Pseudomonas sp. strain DNDY-54 isolated from deep-sea sediment of ninety east ridge 九十东脊深海沉积物中反硝化假单胞菌DNDY-54的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-12-01 DOI: 10.1016/j.margen.2022.100995

Luying Zhao , Yuanyuan Gui , Ao Zhang , Qian Zhang , Liping Fu , Jiang Li

引用次数: 0

Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs 东太平洋珊瑚礁中与挖掘海绵Thoosa mismalolli相关的细菌多样性

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-12-01 DOI: 10.1016/j.margen.2022.100994

Adrián González-Castillo , José Luis Carballo , Eric Bautista-Guerrero

{"title":"Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs","authors":"Adrián González-Castillo , José Luis Carballo , Eric Bautista-Guerrero","doi":"10.1016/j.margen.2022.100994","DOIUrl":"10.1016/j.margen.2022.100994","url":null,"abstract":"<div>Thoosa mismalolli is one of the most abundant and common excavating sponges along Mexican and Central America shallow reefs. This sponge harbors a microbiome unknown so far. In the present study, the metagenome of T. mismalolli was sequenced, and total reads obtained were classified, and contigs were assembled to analyze the microbiota. The results showed that the highest number of contigs was assigned to the phylum ‘Candidatus Poribacteria’ (8848), followed by the phylum Proteobacteria (6415), and Chloroflexi (3972). 22 MAGs with <8.5% redundancy using MaxBin 2 were detected: ‘Candidatus Poribacteria’ (5), Proteobacteria (5), Chloroflexi (6), Gemmatimonadetes (2), Actinobacteria (2), and Thaumarchaeota (2). The phylogenetic tree based on the 139 single-copy gene (SCG) suggested a subdivision into two clades of the phylum Proteobacteria. The presence Thaumarchaeota is also interesting to highlight because contains ammonia-oxidizing archaea considered key members of the global nitrogen and carbon biogeochemical cycles. In addition, shotgun metagenomic analysis revealed that protein sequences associated for amino acids (13.0%) and carbohydrate metabolism (12.4%) predominated. In this study, the first microbiome and functional potential of T. mismalolli is reported, which also represents the first investigation of a microbiota sponge in the Mexican Pacific reefs.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"66 ","pages":"Article 100994"},"PeriodicalIF":1.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40559680","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

Bimodal distribution of seafloor microbiota diversity and function are associated with marine aquaculture 海底微生物群多样性和功能的双峰分布与海洋水产养殖有关

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-12-01 DOI: 10.1016/j.margen.2022.100991

R. Pettersen , I. Ormaasen , I.L. Angell , N.B. Keeley , A. Lindseth , L. Snipen , K. Rudi

{"title":"Bimodal distribution of seafloor microbiota diversity and function are associated with marine aquaculture","authors":"R. Pettersen , I. Ormaasen , I.L. Angell , N.B. Keeley , A. Lindseth , L. Snipen , K. Rudi","doi":"10.1016/j.margen.2022.100991","DOIUrl":"10.1016/j.margen.2022.100991","url":null,"abstract":"<div>The aim of the current work was to investigate the impact of marine aquaculture on seafloor biogeochemistry and diversity from pristine environments in the northern part of Norway. Our analytical approach included analyses of 182 samples from 16 aquaculture sites using 16S and 18S rRNA, shotgun analyses, visual examination of macro-organisms, in addition to chemical measurements. We observed a clear bimodal distribution of the prokaryote composition and richness, determined by analyses of 16S rRNA gene operational taxonomic units (OTUs). The high OTU richness cluster was associated with non-perturbed environments and farness from the aquaculture sites, while the low OTU richness cluster was associated with perturbed environments and proximity to the aquaculture sites. Similar patterns were also observed for eukaryotes using 18S rRNA gene analyses and visual examination, but without a bimodal distribution of OTU richness. Shotgun sequencing showed the archaeum Nitrosopumilus as dominant for the high OTU richness cluster, and the epsilon protobacterium Sulfurovum as dominant for the low OTU richness cluster. Metabolic reconstruction of Nitrosopumilus indicates nitrification as the main metabolic pathway. Sulfurovum, on the other hand, was associated with sulfur oxidation and denitrification. Changes in nitrogen and sulfur metabolism is proposed as a potential explanation for the difference between the high and low OTU richness clusters. In conclusion, these findings suggest that pollution from elevated loads of organic waste drives the microbiota towards a complete alteration of respiratory routes and species composition, in addition to a collapse in prokaryote OTU richness.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"66 ","pages":"Article 100991"},"PeriodicalIF":1.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40363070","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: 1

Transcriptome profiling of the early developmental stages in the giant mussel Choromytilus chorus exposed to delousing drugs 暴露于除蚊药物的巨型贻贝(Choromytilus chorus)早期发育阶段的转录组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-10-01 DOI: 10.1016/j.margen.2022.100970

Gustavo Núñez-Acuña , Camila Fernandez , Sandra Sanhueza-Guevara , Cristian Gallardo-Escárate

{"title":"Transcriptome profiling of the early developmental stages in the giant mussel Choromytilus chorus exposed to delousing drugs","authors":"Gustavo Núñez-Acuña , Camila Fernandez , Sandra Sanhueza-Guevara , Cristian Gallardo-Escárate","doi":"10.1016/j.margen.2022.100970","DOIUrl":"10.1016/j.margen.2022.100970","url":null,"abstract":"<div>The giant mussel Choromytilus chorus is a marine bivalve commonly collected in central – southern Chile from fishery zones shared with the salmon industry. These economically relevant areas are also affected by the use of pesticides for controlling sea lice infestations in salmon aquaculture. Their main target is the sea louse Caligus rogercresseyi. However, other than some physiological impacts, the molecular effects of delousing drugs in non-target species such as C. chorus remain largely understudied. This study aimed to explore the transcriptome modulation of Trochophore and D larvae stages of C. chorus after exposure to azamethiphos and deltamethrin drugs. Herein, RNA-seq analyses and mRNA-lncRNAs molecular interactions were obtained. The most significant changes were found between different larval development stages exposed to delousing drugs. Notably, significant transcriptional variations were correlated with the drug concentrations tested. The biological processes involved in the development, such as cell movement and transcriptional activity, were mainly affected. Long non-coding RNAs (lncRNAs) were also identified in this species, and the transcription activity showed similar patterns with coding mRNAs. Most of the significantly expressed lncRNAs were associated with genes annotated to matrix metalloproteinases, collagenases, and transcription factors. This study suggests that exposure to azamethiphos or deltamethrin drugs can modulate the transcriptome signatures related to the early development of the giant mussel C. chorus.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"65 ","pages":"Article 100970"},"PeriodicalIF":1.9,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40508453","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: 6

Complete genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of Gilvimarinus sp. DA14 isolated from the South China Sea 南海Gilvimarinus sp. DA14的全基因组序列和碳水化合物活性酶库(CAZymes

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-10-01 DOI: 10.1016/j.margen.2022.100982

Qun-Jian Yin , Hong-Zhi Tang , Fang-Chao Zhu , Xu-Yang Chen , De-Wei Cheng , Li-Chang Tang , Xiao-Qing Qi , Xue-Gong Li

{"title":"Complete genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of Gilvimarinus sp. DA14 isolated from the South China Sea","authors":"Qun-Jian Yin , Hong-Zhi Tang , Fang-Chao Zhu , Xu-Yang Chen , De-Wei Cheng , Li-Chang Tang , Xiao-Qing Qi , Xue-Gong Li","doi":"10.1016/j.margen.2022.100982","DOIUrl":"10.1016/j.margen.2022.100982","url":null,"abstract":"<div>Gilvimarinus sp. DA14, a putative new species isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an aerobic and heterotrophic agar degrading bacterium. Here, we present the complete genome sequence of strain DA14, which comprises 3.96 Mb sequences with 53.39% GC content. In total, 3391 CDSs, 6 rRNA genes and 44 tRNA genes were obtained. Genomic analysis of strain DA14 revealed that 218 CAZymes classes were identified and they were organized in 371 CAZymes in PULs involved in polysaccharides degradation, transport and regulation. Further, we performed the genome comparison among Gilvimarinus strains and analysis the diversity of CAZymes and PULs. Meanwhile, ability of agar and alginate degradation in strain DA14 were analyzed. This study represents a thorough genomic characterization of CAZymes repertoire of Gilvimarinus, provides insight into diversity of polysaccharide degrading enzymes existing in Gilvimarinus sp. DA14 and their biotechnological applications.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"65 ","pages":"Article 100982"},"PeriodicalIF":1.9,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33463307","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: 1