Marine genomics最新文献_第3页

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":null,"pages":null},"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":null,"pages":null},"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 the novel Antarctic Oceanisphaera sp. IT1–181 that carried five plasmids 携带 5 个质粒的新型南极海洋矛尾藻 IT1-181 的完整基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2024-01-09 DOI: 10.1016/j.margen.2024.101083

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

{"title":"Complete genome sequence of the novel Antarctic Oceanisphaera sp. IT1–181 that carried five plasmids","authors":"Yong-Qiang Hu , Yi-He Zhang , Wei Han , Ting Hu , Yu Du , Yin-Xin Zeng","doi":"10.1016/j.margen.2024.101083","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101083","url":null,"abstract":"<div>Bacteria of the genus Oceanisphaera in the class Gammaproteobacteria are widely distributed in marine environments. Oceanisphaera sp. IT1–181 was isolated from intertidal sediment in the coastal region of the Chinese Great Wall Station on the Fildes Peninsula, King George Island, Antarctica. Here, we sequenced the complete genome of strain IT1–181, which contained a single chromosome of 3,572,184 bp (G + C content of 49.89 mol%) with five plasmids. A total of 3229 protein-coding genes, 88 tRNA genes, and 25 rRNA genes were obtained. Genome sequence analysis revealed that strain IT1–181 was not only a potentially novel species of the genus Oceanisphaera, but also harbored genes involved in biosynthesizing ectoine as well as poly-β-hydroxybutyric acid (PHB). In addition, genes of a complete type I-E CRISPR–Cas system were found in the bacterium. The results indicate the potential of strain Oceanisphaera sp. IT1–181 in biotechnology and are helpful for us understanding its ecological roles in the changing Antarctic intertidal zone environment.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139398995","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":null,"pages":null},"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

Complete genome sequence of carotenoid-producing Aestuariibaculum lutulentum L182T isolated from the tidal sediment 潮汐沉积物中产类胡萝卜素aestuaribaculum lutulentum L182T的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-11-21 DOI: 10.1016/j.margen.2023.101074

Wen-Jia Liu , Jia-Wei Gao , Yu Zhang , Cong Sun , Lin Xu

{"title":"Complete genome sequence of carotenoid-producing Aestuariibaculum lutulentum L182T isolated from the tidal sediment","authors":"Wen-Jia Liu , Jia-Wei Gao , Yu Zhang , Cong Sun , Lin Xu","doi":"10.1016/j.margen.2023.101074","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101074","url":null,"abstract":"<div>Aestuariibaculum lutulentum L182T (= KCTC 92530T = MCCC 1K08065T) was isolated from the tidal sediment collected in Beihai, People's Republic of China. The genome was sequenced and consisted of a single chromosome with the size of 3,782,725 bp and DNA G + C content of 35.1%. Genomic annotations demonstrated that it encoded 12 rRNA genes, 56 tRNA genes and 3210 ORFs. The percentages of ORFs assigned to CAZy, COG, and KEGG databases were 5.5, 86.2 and 45.5%, respectively. Comparative genomic analysis indicated that the pan- and core-genomes of the genus Aestuariibaculum consisted of 4826 and 2257 orthologous genes, respectively. Carbohydrate-active enzyme annotations of the genus Aestuariibaculum genomes revealed that they shared three polysaccharide lyase (PL) families including PL1, PL22 and PL42. Meanwhile, one carotenoid biosynthetic gene cluster related to biosynthesizing flexixanthin was found in the genus Aestuariibaculum. Furthermore, the core-genome of the genus Aestuariibaculum showed that this genus played a role in cleaving pectate, degrading ulvan, and biosynthesizing carotenoids. This study is a complete genomic report of the genus Aestuariibaculum and broadens understandings of its ecological roles and biotechnological applications.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138403984","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 type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater 温热杆菌科新菌株类型的全基因组分析。11月，与表层海水隔离

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-11-06 DOI: 10.1016/j.margen.2023.101073

Jin-Cheng Rong , Lin-Lin Cui , Xiao-Chen Yang , Mao-Li Yi , Qi Zhao

{"title":"Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater","authors":"Jin-Cheng Rong , Lin-Lin Cui , Xiao-Chen Yang , Mao-Li Yi , Qi Zhao","doi":"10.1016/j.margen.2023.101073","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101073","url":null,"abstract":"<div>Novel bacterial resources are valuable for studying bacterial taxonomy, bacterial evolution, and genome mining of novel antibiotics, antitumor agents, and immune modulators. In this study, we de novo sequenced the type strain of a novel bacterial family, Temperatibacteraceae fam. Nov., belonging to class Alphaproteobacteria of phylum Pseudomonadota. The type strain, Temperatibacter marinus NBRC 110045T, is mesophilic and was isolated from surface seawater around Muroto city of Japan at a depth of 0.5 m. Here, the sequenced complete genome of strain NBRC 110045T is composed of a circular chromosome of 3,184,799 bp with a mean G + C content of 43.71%. Genome analysis was applied to reveal the genetic basis of its cellular activities. Cellular regulation and signaling was analyzed to infer the regulatory mechanism of its limited growth temperature range. Genomic features of the novel family Temperatibacteraceae may expand our knowledge on environmental adaptation, genetic evolution and natural product discovery of marine bacteria.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91593845","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

The complete genome sequence of Peribacillus sp. R9–11 for genome mining of polystyrene degrading enzymes 为聚苯乙烯降解酶的基因组挖掘提供了芽孢杆菌R9-11的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-20 DOI: 10.1016/j.margen.2023.101072

Xue Yu , Wenbin Guo , Jingjing Duan

引用次数: 0

Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean 西太平洋烟草黑胫病生物防治剂蜡样芽孢杆菌Z4的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-13 DOI: 10.1016/j.margen.2023.101071

Shunhua Ji , Yin Tian , Jingjing Li , Guangxin Xu , Yongan Zhang , Shanyi Chen , Yiqiang Chen , Xixiang Tang

{"title":"Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean","authors":"Shunhua Ji , Yin Tian , Jingjing Li , Guangxin Xu , Yongan Zhang , Shanyi Chen , Yiqiang Chen , Xixiang Tang","doi":"10.1016/j.margen.2023.101071","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101071","url":null,"abstract":"<div>Bacillus species have been considered as promising biological control agents due to their excellent antimicrobial ability. Bacillus cereus strain Z4 was isolated from 2000 m deep sea sediments of the Western Pacific Ocean, which possesses significant antifungal activity against Phytophthora nicotianae, the pathogenic fungus of tobacco black shank disease. To reveal the underlying antifungal genetic mechanisms, here, we report the complete genomic sequence of the strain Z4. The genome has one circular chromosome of 5,664,309 bp with a G + C content of 35.31%, 109 tRNAs, and 43 rRNAs. Genomic analysis identified 10 gene clusters related to the biosynthesis of biocontrol active compounds, including bacillibactin, petrobactin, fengycin, and molybdenum cofactor. Meanwhile, 6 gene clusters were responsible for the biosynthesis of metabolites with unknown functions. Strain Z4 also contains a large number of genes encoding carbohydrate-active enzymes and secreted proteins, respectively. The whole genomic analysis of Bacillus cereus Z4 may provide a valuable reference for elucidating its biocontrol mechanism against tobacco black shank.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49886267","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

Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia 蓝贻贝(Mytilus edulis)对急性缺氧的大小和位点特异性转录组反应

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101060

Stephanie Hall , Denise Méthé , Sarah Stewart-Clark , Fraser Clark

{"title":"Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia","authors":"Stephanie Hall , Denise Méthé , Sarah Stewart-Clark , Fraser Clark","doi":"10.1016/j.margen.2023.101060","DOIUrl":"10.1016/j.margen.2023.101060","url":null,"abstract":"<div>The Prince Edward Island (PEI) mussel aquaculture industry is being challenged by climate change induced environmental stressors including hypoxic/anoxic episodes, that can impact mussel health and survival. Physiological responses of mussels to hypoxia/anoxia have been studied; however, less is known about how transcriptomic response leads to physiology. The present study examined the transcriptomic response of acute (4 h) hypoxia in blue mussels (Mytilus edulis) from two sites and size classes in PEI, Canada. Overall, major changes in whole-mussel transcriptomics associated with metabolism, cellular organelles/processes and environmental sensing were observed in the first hours of hypoxia exposure. Differences in differentially expressed transcripts were observed between each site and size, indicating that responses to acute hypoxia exposure are highly complex. A size related pattern was observed, with seed size mussels having differential expression of transcripts associated with development, muscle function, and byssal attachment compared to the adults. Adult mussels had higher HSP 90 expression, while HSPs were predominately under-expressed in seed mussels. Seed mussels had significant under-expression of several classes of byssal thread attachment transcripts, indicating a decline in the production of byssal thread or detachment, both which have negative consequences for mussel aquaculture.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10079475","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 reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum 硫氧化细菌Thioclava nitratireducens M1-LQ-LJL-11的全基因组分析及其与深海热液喷口Chrysomallon squamiferum的共生关系

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101058

Xin Yin , Xiang Li , Qian Li , Bingshu Wang , Li Zheng

{"title":"Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum","authors":"Xin Yin , Xiang Li , Qian Li , Bingshu Wang , Li Zheng","doi":"10.1016/j.margen.2023.101058","DOIUrl":"10.1016/j.margen.2023.101058","url":null,"abstract":"<div>One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10078909","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