Marine genomics最新文献

{"title":"Complete genome sequencing and analysis revealed the nitrogen utilization strategy of a novel Acuticoccus species isolated from surface water of the Indian Ocean","authors":"Jie Shi ,&nbsp;Yufeng Zeng ,&nbsp;Huan Wang ,&nbsp;Yuanyuan Niu ,&nbsp;Peiqing He ,&nbsp;Hao Chen","doi":"10.1016/j.margen.2022.100971","DOIUrl":"10.1016/j.margen.2022.100971","url":null,"abstract":"<div><p><em>Acuticoccus</em> sp. I52.16.1 was isolated from 100 m water depth from the Indian Ocean, and presented a novel <em>Acuticoccus</em> species belonging to the family Acuticoccaceae, class Alphaproteobacteria. The strain I52.16.1 displayed the activities of nitrate reductase, nitrite reductase, and urease. The genome of <em>Acuticoccus</em> sp. I52.16.1 consisted of a circular chromosome (5, 134, 086<!--> <!-->bp) with a G + C content of 69.7 mol%. The predicted number of coding genes was 4935, including 6 rRNA, 47 tRNA, and 2 sRNA. The 16S rDNA sequence displayed the maximum similarity of 97.58% with <em>Acuticoccus yangtzensis</em> JL1095^T, followed by <em>Acuticoccus sediminis</em> PTG4-2^T (97.05%), <em>Acuticoccus kandeliae</em> J103^T (96.52%), and <em>Acuticoccus mangrove</em> B2012^T (95.85%). <em>Acuticoccus</em> sp. I52.16.1 contained clades of genes involved in assimilating ammonium, nitrate, nitrite, and simple organic nitrogen compounds, but lacked the pathway for dissimilatory denitrification. Two distinct types of ureases were also detected, suggesting genetic heterogeneity. This study provided insight into the nitrogen metabolism strategies of heterotrophic bacteria in the oligotrophic ocean surface.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33463306","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}

{"title":"Transcriptome responses in copepods Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus exposed to phenanthrene and benzo[a]pyrene","authors":"Fekadu Yadetie ,&nbsp;Nadja R. Brun ,&nbsp;Julia Giebichenstein ,&nbsp;Katarzyna Dmoch ,&nbsp;Ketil Hylland ,&nbsp;Katrine Borgå ,&nbsp;Odd André Karlsen ,&nbsp;Anders Goksøyr","doi":"10.1016/j.margen.2022.100981","DOIUrl":"10.1016/j.margen.2022.100981","url":null,"abstract":"<div><p>Arctic and sub-arctic pelagic organisms can be exposed to effluents and spills from offshore petroleum-related activities and thus it is important to understand how they respond to crude oil related contaminants such as polycyclic aromatic hydrocarbons (PAHs). The copepod species <em>Calanus finmarchicus, Calanus glacialis</em> and <em>Calanus hyperboreus</em> represent key links in the arctic marine food web. We performed a transcriptome analysis of the three species exposed to phenanthrene (Phe) and benzo[<em>a</em>]pyrene (BaP) representing low and high molecular weight PAHs, respectively. Differential expression of several genes involved in many cellular pathways was observed after 72 h exposure to Phe (0.1 μM) and BaP (0.1 μM). In <em>C. finmarchicus</em> and <em>C. glacialis</em>, the exposure resulted in up-regulation of genes encoding enzymes in xenobiotic biotransformation, particularly the phase II cytosolic sulfonation system that include 3′-phosphoadenosine 5′-phosphosulfate synthase (PAPSS) and sulfotransferases (SULTs). The sulfonation pathway genes were more strongly induced by BaP than Phe in <em>C. finmarchicus</em> and <em>C. glacialis</em> but were not affected in <em>C. hyperboreus</em>. However, a larger number of genes and pathways were modulated in <em>C. hyperboreus</em> by the PAHs including genes encoding xenobiotic biotransformation and lipid metabolism enzymes, suggesting stronger responses in this species. The results suggest that the cytosolic sulfonation is a major phase II conjugation pathway for PAHs in <em>C. finmarchicus</em> and <em>C. glacialis</em>. Some of the biotransformation systems affected are known to be involved in metabolism of endogenous compounds such as ecdysteroids, which may suggest potential interference with physiological and developmental processes of the copepod species.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874778722000599/pdfft?md5=5318cd15fd32225027dedd984991b635&pid=1-s2.0-S1874778722000599-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40616202","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}

{"title":"Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition","authors":"Zoya Harbuzov ,&nbsp;Valeria Farberova ,&nbsp;Moshe Tom ,&nbsp;Alberto Pallavicini ,&nbsp;David Stanković ,&nbsp;Tamar Lotan ,&nbsp;Hadas Lubinevsky","doi":"10.1016/j.margen.2022.100980","DOIUrl":"10.1016/j.margen.2022.100980","url":null,"abstract":"<div><p><span>The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470–490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as </span>metabarcoding reference library. It contained 461 ASVs and 342–3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40695402","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}

{"title":"Aquaculture omics: An update on the current status of research and data analysis","authors":"Jitendra Kumar Sundaray ,&nbsp;Sangita Dixit ,&nbsp;Ashraf Rather ,&nbsp;Kiran D. Rasal ,&nbsp;Lakshman Sahoo","doi":"10.1016/j.margen.2022.100967","DOIUrl":"10.1016/j.margen.2022.100967","url":null,"abstract":"<div><p>Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing<span><span><span><span> technology has revolutionized the biological sciences and provided necessary tools. Application of ‘omics’ in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of </span>single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, </span>transcriptome<span><span> profiling and miRNAs<span> analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome<span><span> analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. </span>Metagenomics has been successfully used in the aquaculture sector to identify novel and potential </span></span></span>pathogens<span>, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, </span></span></span>probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.</span></p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40465401","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}

{"title":"Transcriptome analysis of the ink sac and brain tissues from Sepiella inermis: A resource for discovering genes related to the inking of cephalopods","authors":"Shanshan Zhou ,&nbsp;Tao Zhang ,&nbsp;Cuili Wang ,&nbsp;Jun Liang ,&nbsp;Pengfei Li ,&nbsp;Kaida Xu ,&nbsp;Hengtong Qiu","doi":"10.1016/j.margen.2022.100968","DOIUrl":"10.1016/j.margen.2022.100968","url":null,"abstract":"<div><p>The common Chinese cuttlefish (<em>Sepiella inermis</em>) is an important cephalopod with nutritional and commercial value. Intensive inking stimulated by swilling seawater in transfer containers threatens the survival of cephalopods during transportation. However, the molecular basis for the inking behavior of <em>S. inermis</em> remains unclear. In the present study, transcriptome analysis was performed on ink sac and brain tissues from <em>S. inermis</em> under two different conditions, i.e. the control group (with individuals immersed in static seawater) and the experimental group (with individuals immersed in swilling seawater) to determine the global gene expression differences. The individuals from the experimental group ejected ink in response to the swilling of seawater. 330,699 unigenes were obtained from twelve transcriptome libraries via the Illumina Hiseq X platform, and the differentially expressed genes in the ink sac and brain tissues were identified respectively. Multiple upregulated genes in the ink sac were involved in cation transporter activity. Besides, an autocrine/paracrine factor <em>wnt10b like</em> and two important transcription factors (<em>homeobox 1</em> and <em>Hes-1-b-like</em>) were also significantly upregulated in the ink sac. Moreover, a neuronal nitric oxide synthase (nNOS) was significantly downregulated in the brain. The findings from this study provide an important transcriptomic resource for discovering critical genes related to inking behavior of <em>S. inermis</em>, providing a basis for developing potential methods for protecting <em>S. inermis</em> from intensive inking.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874778722000460/pdfft?md5=b54796d83b078a8313868c8dd3e40fb7&pid=1-s2.0-S1874778722000460-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40460734","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}

{"title":"Complete genome sequence of Devosia beringensis S02T, a type strain with genes involved in deoxynivalenol degradation","authors":"Pu-Yu Hao ,&nbsp;Hui-Rong Li ,&nbsp;Wei Luo ,&nbsp;Ren Xu ,&nbsp;Yin-Xin Zeng","doi":"10.1016/j.margen.2022.100969","DOIUrl":"https://doi.org/10.1016/j.margen.2022.100969","url":null,"abstract":"<div><p>Members of the genus <em>Devosia</em> are known for their abilities to degrade deoxynivalenol (DON). The type strain <em>Devosia beringensis</em> S02^T (= JCM 33772 = CCTCC AB 2019343) was isolated from sediment of the Bering Sea and identified in 2021. However, the genome sequence of <em>D. beringensis</em> S02^T remains unclear, which complicates the exploration into the function and ecological role of this strain in marine sediment. The genome of <em>D. beringensis</em> S02^T contained a 4,048,765 bp chromosome with a G + C content of 63.84 mol%. Potential genes involved in DON degradation were found in the genome. In addition, multiple genes involved in polysaccharide degradation, including agarose, chitin, carrageen, pectate, starch, and xylan, were also annotated in the genome. These findings indicated the potential of strain S02^T to be used for DON degradation and its ecological function in the carbon cycle in marine sediment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72076232","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}

{"title":"Genomic analysis of Shewanella eurypsychrophilus YLB-09 reveals backgrounds related to its deep sea environment adaptation","authors":"Xiaorong Cao ,&nbsp;Zhiwei Yi ,&nbsp;Xu Qiu ,&nbsp;Huangming Wu ,&nbsp;Libo Yu ,&nbsp;Xixiang Tang","doi":"10.1016/j.margen.2022.100956","DOIUrl":"10.1016/j.margen.2022.100956","url":null,"abstract":"<div><p><em>Shewanella eurypsychrophilus</em> YLB-09 is a psychrophilic and piezotolerant bacterium that was isolated from 2699 m deep sea sediments of the Southwest Indian Ocean. The complete genome sequence of the strain <em>Shewanella eurypsychrophilus</em> YLB-09 was analyzed. The genome of <em>Shewanella eurypsychrophilus</em> YLB-09 contained one single circular chromosome 6,225,487 base pairs with a 43.6 mol% G + C content of 52 ribosomal RNA genes and 5124 protein-coding genes. YLB-09 has the largest number of genes related to energy production and conversion among 22 available complete genomes of <em>Shewanella</em> genus. Meanwhile， a large quantity of genes encoding flagellum/fimbrial-related proteins and two major secondary metabolic gene clusters were found in YLB-09. These data could provide insights into the mechanism of this strain in adapting to deep sea extreme environments.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40577288","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}

{"title":"Transcriptomic response of intertidal brittle star Ophiothrix exigua to seasonal variation","authors":"Md. Tariful Islam Fuad ,&nbsp;Wenge Shi ,&nbsp;Xiaomei Liao ,&nbsp;Yixuan Li ,&nbsp;S.M. Sharifuzzaman ,&nbsp;Xuelei Zhang ,&nbsp;Xiaoshou Liu ,&nbsp;Qinzeng Xu","doi":"10.1016/j.margen.2022.100957","DOIUrl":"10.1016/j.margen.2022.100957","url":null,"abstract":"<div><p><span>Adaptation to seasonal change is essential for survival, and is especially critical for organisms living in physically harsh environments. Brittle stars (</span><em>Ophiothrix</em><span>), known as a keystone species<span>, inhabiting the intertidal rocky ecosystem are affected by multiple stressors, but molecular insights into their adaptation remain poorly studied. In the present study, transcriptomic responses of </span></span><em>Ophiothrix exigua</em><span> from the intertidal habitats of the North Pacific Ocean during summer and winter are reported. A total of 12,844 differentially expressed genes (DEGs) were identified. Of these, 7102 genes were up-regulated and 5742 genes were down-regulated in summer relative to winter. One hundred fifty-two key DEGs, including 31 up-regulated and 121 down-regulated genes, were categorized into three major subcategories and seven subclasses. The key DEGs included </span><em>heat shock cognate protein 70</em> (<em>HSC70</em>), <em>toll-like receptor-2</em> (<em>TLR2</em>), <span><span><em>cAMP-dependent protein kinase </em><em>catalytic subunit</em><em> beta-like </em></span><em>isoform</em><em> X2</em></span> (<em>PKA</em>), <span><em>serine/threonine-protein kinase </em><em>mTOR</em></span> (<em>MTOR</em>), and <span><em>ras-related c3 </em><em>botulinum toxin</em><em> substrate 1 isoform X1</em></span> (<span><em>RAC1</em></span>). <span><em>Glutathione</em><em> peroxidase-like</em></span> (<em>GPX</em>) and <em>tubulin</em> superfamily members (<em>TUBA</em>, <em>TUBB</em><span>) were consistent across seasons. The main defense-related pathways in brittle star were phagosome, apoptosis, and glutathione metabolism. These findings would greatly enhance our understanding of the genomic basis of environmental adaptation in intertidal invertebrates.</span></p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43290497","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}

{"title":"Complete genome sequence of marine photoheterotophic bacterium Erythrobacter sp. JK5","authors":"So-Jeong Kim ,&nbsp;Minji Kim ,&nbsp;Ki-Eun Lee ,&nbsp;In-Tae Cha ,&nbsp;Soo-Je Park","doi":"10.1016/j.margen.2022.100950","DOIUrl":"10.1016/j.margen.2022.100950","url":null,"abstract":"<div><p><em>Erythrobacter</em> sp. JK5, a marine heterotrophic bacterium, was isolated from marine sediment in Jeju island, the Republic of Korea. Here, we report information on the complete genome of strain JK5, including a putative capability for photosynthesis. The genome of JK5 consisted of 3.34 Mbp with 64.2% G + C content, and contained 3210 protein-coding sequences and three rRNA genes. Genomic analysis revealed that strain JK5 might be grown under oxic, microoxic, or anoxic conditions using two types of terminal oxidase (high and low oxygen affinity) or nitrate reductase. The types IV and VI secretion systems presented in strain JK5 genome might reveal a survival advantage against their ecological competitors in the marine environment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47871231","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}

{"title":"First certain record of Demospongiae class (Porifera) alien species from the Mediterranean Sea","authors":"Marco Bertolino ,&nbsp;Gabriele Costa ,&nbsp;Nadia Ruocco ,&nbsp;Roberta Esposito ,&nbsp;Sergio De Matteo ,&nbsp;Giacomo Zagami ,&nbsp;Maria Costantini","doi":"10.1016/j.margen.2022.100951","DOIUrl":"10.1016/j.margen.2022.100951","url":null,"abstract":"<div><p>In this paper, we identify some sponge specimens collected in the Faro Lake in Sicily, and belonging to <em>Haliclona</em> (<em>Halicoclona</em><span>) by using morphological analysis accompanied by molecular analysis through amplification of several molecular markers (18S and 28S rRNA, CO1 and ITS).</span></p><p>The samples are identified as. <em>H</em>. (<em>Halichoclona</em>) <em>vansoesti</em><span> de Weerdt, de Kluijver &amp; Gómez, 1999, a species native to the Caribbean, and therefore this is the first record of an alien species of the Demospongiae class (Porifera) from the Mediterranean Sea. This presence can be ascribed as results of global change (mainly global warming) that are affecting marine environment.</span></p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54838964","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}