Marine genomics最新文献_第10页

Aquaculture omics: An update on the current status of research and data analysis 水产养殖组学:最新的研究现状和数据分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-08-01 DOI: 10.1016/j.margen.2022.100967

Jitendra Kumar Sundaray , Sangita Dixit , Ashraf Rather , Kiran D. Rasal , Lakshman Sahoo

{"title":"Aquaculture omics: An update on the current status of research and data analysis","authors":"Jitendra Kumar Sundaray , Sangita Dixit , Ashraf Rather , Kiran D. Rasal , Lakshman Sahoo","doi":"10.1016/j.margen.2022.100967","DOIUrl":"10.1016/j.margen.2022.100967","url":null,"abstract":"<div>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 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 single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs 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 analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"64 ","pages":"Article 100967"},"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}

引用次数: 6

Transcriptome analysis of the ink sac and brain tissues from Sepiella inermis: A resource for discovering genes related to the inking of cephalopods 无足seppiella inmis墨迹囊和脑组织的转录组分析:发现与头足类墨迹相关的基因的资源

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-08-01 DOI: 10.1016/j.margen.2022.100968

Shanshan Zhou , Tao Zhang , Cuili Wang , Jun Liang , Pengfei Li , Kaida Xu , Hengtong Qiu

{"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 , Tao Zhang , Cuili Wang , Jun Liang , Pengfei Li , Kaida Xu , Hengtong Qiu","doi":"10.1016/j.margen.2022.100968","DOIUrl":"10.1016/j.margen.2022.100968","url":null,"abstract":"<div>The common Chinese cuttlefish (Sepiella inermis) 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 S. inermis remains unclear. In the present study, transcriptome analysis was performed on ink sac and brain tissues from S. inermis 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 wnt10b like and two important transcription factors (homeobox 1 and Hes-1-b-like) 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 S. inermis, providing a basis for developing potential methods for protecting S. inermis from intensive inking.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"64 ","pages":"Article 100968"},"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}

引用次数: 0

Complete genome sequence of Devosia beringensis S02T, a type strain with genes involved in deoxynivalenol degradation 具有脱氧雪腐镰刀菌烯醇降解相关基因的模式菌株白灵草属S02T的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-08-01 DOI: 10.1016/j.margen.2022.100969

Pu-Yu Hao , Hui-Rong Li , Wei Luo , Ren Xu , Yin-Xin Zeng

引用次数: 1

Transcriptomic response of intertidal brittle star Ophiothrix exigua to seasonal variation 潮间带蛇尾对季节变化的转录组反应。

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-08-01 DOI: 10.1016/j.margen.2022.100957

Md. Tariful Islam Fuad , Wenge Shi , Xiaomei Liao , Yixuan Li , S.M. Sharifuzzaman , Xuelei Zhang , Xiaoshou Liu , Qinzeng Xu

{"title":"Transcriptomic response of intertidal brittle star Ophiothrix exigua to seasonal variation","authors":"Md. Tariful Islam Fuad , Wenge Shi , Xiaomei Liao , Yixuan Li , S.M. Sharifuzzaman , Xuelei Zhang , Xiaoshou Liu , Qinzeng Xu","doi":"10.1016/j.margen.2022.100957","DOIUrl":"10.1016/j.margen.2022.100957","url":null,"abstract":"<div>Adaptation to seasonal change is essential for survival, and is especially critical for organisms living in physically harsh environments. Brittle stars (Ophiothrix), known as a keystone species, 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 Ophiothrix exigua 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 heat shock cognate protein 70 (HSC70), toll-like receptor-2 (TLR2), cAMP-dependent protein kinase catalytic subunit beta-like isoform X2 (PKA), serine/threonine-protein kinase mTOR (MTOR), and ras-related c3 botulinum toxin substrate 1 isoform X1 (RAC1). Glutathione peroxidase-like (GPX) and tubulin superfamily members (TUBA, TUBB) 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.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"64 ","pages":"Article 100957"},"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}

引用次数: 3

Genomic analysis of Shewanella eurypsychrophilus YLB-09 reveals backgrounds related to its deep sea environment adaptation eurypsychrophilus Shewanella YLB-09基因组分析揭示了其适应深海环境的相关背景

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-08-01 DOI: 10.1016/j.margen.2022.100956

Xiaorong Cao , Zhiwei Yi , Xu Qiu , Huangming Wu , Libo Yu , Xixiang Tang

引用次数: 0

Complete genome sequence of marine photoheterotophic bacterium Erythrobacter sp. JK5 海洋光异养细菌红杆菌sp. JK5全基因组序列。

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-06-01 DOI: 10.1016/j.margen.2022.100950

So-Jeong Kim , Minji Kim , Ki-Eun Lee , In-Tae Cha , Soo-Je Park

引用次数: 0

First certain record of Demospongiae class (Porifera) alien species from the Mediterranean Sea 首个来自地中海的Demospongiae (Porifera)外来物种记录

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-06-01 DOI: 10.1016/j.margen.2022.100951

Marco Bertolino , Gabriele Costa , Nadia Ruocco , Roberta Esposito , Sergio De Matteo , Giacomo Zagami , Maria Costantini

引用次数: 0

Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes 采样和储存方式对海带微生物组16S rDNA扩增子测序结果的影响

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-06-01 DOI: 10.1016/j.margen.2022.100944

Bertille Burgunter-Delamare , Gwenn Tanguy , Erwan Legeay , Catherine Boyen , Simon M. Dittami

{"title":"Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes","authors":"Bertille Burgunter-Delamare , Gwenn Tanguy , Erwan Legeay , Catherine Boyen , Simon M. Dittami","doi":"10.1016/j.margen.2022.100944","DOIUrl":"10.1016/j.margen.2022.100944","url":null,"abstract":"<div>Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"63 ","pages":"Article 100944"},"PeriodicalIF":1.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47639013","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: 3

Complete genome sequence of Streptomyces malaysiensis HNM0561, a marine sponge-associated actinomycete producing malaymycin and mccrearamycin E 产马来霉素和麦克雷霉素E的海洋海绵相关放线菌马来西亚链霉菌HNM0561的全基因组序列。

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-06-01 DOI: 10.1016/j.margen.2022.100947

Ji Zhu , Yuhui Xie , Yu Li , Yuxin Yang , Chengui Li , Dongyi Huang , Wenqiang Wu , Yun Xu , Wei Xia , Xiaolong Huang , Shuangqing Zhou

{"title":"Complete genome sequence of Streptomyces malaysiensis HNM0561, a marine sponge-associated actinomycete producing malaymycin and mccrearamycin E","authors":"Ji Zhu , Yuhui Xie , Yu Li , Yuxin Yang , Chengui Li , Dongyi Huang , Wenqiang Wu , Yun Xu , Wei Xia , Xiaolong Huang , Shuangqing Zhou","doi":"10.1016/j.margen.2022.100947","DOIUrl":"10.1016/j.margen.2022.100947","url":null,"abstract":"<div>Streptomyces malaysiensis HNM0561 is a marine sponge-associated actinomycete with the potential to produce potential anti-androgens against prostate cancer cells, including malaymycin and mccrearamycin E. Here, we present the complete genome sequence of S. malaysiensis HNM0561, which consists of a linear chromosome of 11,656,895 bp and a circular plasmid of 32,797 bp, 9849 protein coding genes, 18 rRNA genes, 66 tRNA genes, and 191 sRNA genes. Genomic annotations revealed that 72.03% of the protein-coding genes were assigned to the COG database, among which the abundant genes were predicted to be involved in transcription, replication, carbohydrate transport and metabolism, and amino acid transport and metabolism. Forty-nine putative secondary metabolite biosynthetic gene clusters were found in the genome. Among them, the potential biosynthetic gene clusters of malaymycin and mccrearamycin E have been described respectively. The complete genome information presented here will enable us to investigate the biosynthetic mechanism of two novel structures of malaymycin and mccrearamycin E and to discover novel secondary metabolites with potential against prostate cancer cell activities.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"63 ","pages":"Article 100947"},"PeriodicalIF":1.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42802114","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

Iso-Seq assembly and functional annotation of full-length transcriptome of turbot (Scophthalmus maximus) during bacterial infection 大菱鲆细菌感染过程中全长转录组的Iso-Seq组装与功能注释

IF 1.9 4区生物学

Marine genomics Pub Date : 2022-06-01 DOI: 10.1016/j.margen.2022.100954

Jianchang Huang , Weijie Chen , Qiyao Wang , Yuanxing Zhang , Qin Liu , Dahai Yang

{"title":"Iso-Seq assembly and functional annotation of full-length transcriptome of turbot (Scophthalmus maximus) during bacterial infection","authors":"Jianchang Huang , Weijie Chen , Qiyao Wang , Yuanxing Zhang , Qin Liu , Dahai Yang","doi":"10.1016/j.margen.2022.100954","DOIUrl":"10.1016/j.margen.2022.100954","url":null,"abstract":"<div>Turbot (Scophthalmus maximus) is a flatfish, which is not only important in mariculture worldwide with the unique characteristic of body asymmetry, but also as an economically important species in aquaculture. Herein, we performed the first full-length transcriptome sequencing of turbot during the bacterial infection. A total of 307.1 Gb raw reads were obtained and processed with Iso-Seq, generating 187,509 high-quality redundant transcripts with an average length of 3005 base pairs. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis identified 81.5% complete BUSCOs and only 1.7% fragmented BUSCOs, suggesting a transcript structural completeness and functional diversity of this transcriptome. Moreover, the redundant transcripts were collapsed and compared to ENSEMBL reference with Cupcake and SQANTI3. Among 60,476 collapsed transcripts, we identified 12,059 annotated and 1684 novel genes. 42,956 (71.1%) transcripts provided new evidence for splice junctions identification. Furthermore, the untranslated region (UTR) identification was also benefited from the transcriptome. The open read frames prediction was conducted with PASApipeline. 42,118 transcripts were assigned with known function by aligning against Swiss-Prot or functional domain prediction. Taken together, the full-length transcriptome built in this study could provide important resources for immunologic research on turbot.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"63 ","pages":"Article 100954"},"PeriodicalIF":1.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41740933","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: 2