journal
https://read.qxmd.com/read/38301367/de-novo-transcriptome-sequencing-and-annotation-of-the-antarctic-polychaete-microspio-moorei-spionidae-with-its-characterization-of-the-heat-stress-related-proteins-hsp-sod-cat
#1
JOURNAL ARTICLE
Idalyd Fonseca-González, Esteban Velasquez-Agudelo, Mario H Londoño-Mesa, Javier C Álvarez
We present a de novo transcriptome assembly for the non-model Antarctic polychaete worm Microspio moorei (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for Microspio spp. The gene sequences of the spionid worm were annotated from a wide range of functions (i.e., biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes...
January 31, 2024: Marine Genomics
https://read.qxmd.com/read/38485293/complete-genome-sequence-of-the-novel-antarctic-oceanisphaera-sp-it1-181-that-carried-five-plasmids
#2
JOURNAL ARTICLE
Yong-Qiang Hu, Yi-He Zhang, Wei Han, Ting Hu, Yu Du, Yin-Xin Zeng
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...
April 2024: Marine Genomics
https://read.qxmd.com/read/38485292/a-whole-body-transcriptome-assembly-of-the-annelid-worm-hediste-diversicolor
#3
JOURNAL ARTICLE
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
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...
April 2024: Marine Genomics
https://read.qxmd.com/read/38485291/an-historical-wreck-a-transcriptome-assembly-of-the-naval-shipworm-teredo-navalis-linnaeus-1978
#4
JOURNAL ARTICLE
André Gomes-Dos-Santos, Marcos Domingues, Raquel Ruivo, Elza Fonseca, Elsa Froufe, Diana Deyanova, João N Franco, L Filipe C Castro
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...
April 2024: Marine Genomics
https://read.qxmd.com/read/38485290/complete-genome-sequence-of-psychrobacter-cibarius-aosw16051-a-trimeric-autotransporter-adhesin-synthesizing-bacterium-isolated-from-the-baltic-sea
#5
JOURNAL ARTICLE
Xiao-Yu Wang, Tianyin Miao, Yuyi Wang, Zhangwei Guo, Jin-Long Yang, Xiao Liang
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...
April 2024: Marine Genomics
https://read.qxmd.com/read/38365348/reference-transcriptome-assembly-of-a-protogynous-sex-change-fish-harlequin-sandsmelt-parapercis-pulchella
#6
JOURNAL ARTICLE
Akifumi Yao, Hisanori Kohtsuka, Toru Miura
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...
February 2024: Marine Genomics
https://read.qxmd.com/read/38365347/complete-genome-sequence-analysis-of-bacillus-velezensis-a5-a-promising-biocontrol-agent-from-the-pacific-ocean
#7
JOURNAL ARTICLE
Shunhua Ji, Yin Tian, Guangxin Xu, Yiqiang Chen, Jingjing Li, Teng Long, Wei He, Jianqiang Fan, Xixiang Tang
Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is a serious soil-borne disease, which seriously damages the growth of tobacco crops. Bacillus velezensis A5 was isolated from 3000 m deep-sea sediments of the Pacific Ocean, and was found to be antagonistic to TBW. Here, we report the complete genome sequence of strain A5, which has a 4,000,699-bp single circular chromosome with 3827 genes and a G + C content of 46.44%, 87 tRNAs, and 27 rRNAs. A total of 12 gene clusters were identified in the genome of strain A5, which were responsible for the biosynthesis of antibacterial compounds, including surfactin, bacillaene, fengycin, difficidin, bacillibactin, and bacilysin...
February 2024: Marine Genomics
https://read.qxmd.com/read/38008534/complete-genome-sequence-of-carotenoid-producing-aestuariibaculum-lutulentum-l182-t-isolated-from-the-tidal-sediment
#8
JOURNAL ARTICLE
Wen-Jia Liu, Jia-Wei Gao, Yu Zhang, Cong Sun, Lin Xu
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...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008533/complete-genome-sequence-of-bacillus-cereus-z4-a-biocontrol-agent-against-tobacco-black-shank-isolated-from-the-western-pacific-ocean
#9
JOURNAL ARTICLE
Shunhua Ji, Yin Tian, Jingjing Li, Guangxin Xu, Yongan Zhang, Shanyi Chen, Yiqiang Chen, Xixiang Tang
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...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008532/complete-genome-analysis-of-type-strain-of-a-novel-bacterial-family-temperatibacteraceae-fam-nov-isolated-from-surface-seawater
#10
JOURNAL ARTICLE
Jin-Cheng Rong, Lin-Lin Cui, Xiao-Chen Yang, Mao-Li Yi, Qi Zhao
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...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008531/the-complete-genome-sequence-of-peribacillus-sp-r9-11-for-genome-mining-of-polystyrene-degrading-enzymes
#11
JOURNAL ARTICLE
Xue Yu, Wenbin Guo, Jingjing Duan
Peribacillus sp. R9-11, isolated from a marine sediment sample of the Arctic Ocean, can grow in mineral medium with polystyrene (PS) plastic as sole carbon source. Here, we present the complete genome of Peribacillus sp. R9-11, which will facilitate the genome mining of PS degrading enzymes. The total length of the sequenced genome consists of 6,288,471 bases, with mean G + C content of 37.93%. A total of 6447 coding genes including 84 tRNAs and 37 rRNAs were predicted in the genome. Some potential PS degrading enzymes including cytochrome P450s and peroxidases were found in this genome...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008530/genomic-analysis-of-a-marine-alphaproteobacterium-sagittula-sp-strain-ma-2-that-carried-eight-plasmids
#12
JOURNAL ARTICLE
Mayuko Abe, Robert A Kanaly, Jiro F Mori
Bacteria that belong to the family Roseobacteraceae in the Alphaproteobacteria class are widely distributed in marine environments with remarkable physiological diversity, which is considered to be attributed to their genomic plasticity. In this study, a novel isolate of the genus Sagittula within Roseobacteraceae, strain MA-2, was obtained from a coastal marine bacterial consortium enriched with aromatic hydrocarbons, and its complete genome was sequenced. The genome with a total size of 5.69 Mbp was revealed to consist of a 4...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008529/characterization-and-genomic-analysis-of-a-novel-pseudoalteromonas-phage-ps_l5
#13
JOURNAL ARTICLE
Xing Zhou, Jie Gao, Rongda Xiao, Yifan Qiao, Yuang Zhu, Di Zhang, Xinyu Zhang, Huifang Li, Juntian Xu
Pseudoalteromonas is a widely distributed bacterial genus that is associated with marine algae. However, there is still limited knowledge about their bacteriophage. In this study, we reported the isolation of a novel lytic bacteriophage that infects Pseudoalteromonas marina. Transmission electron microscopy revealed that PS_L5 had an icosahedral head of 52.6 ± 2 nm and a non-contractile tail with length of 96.5 ± 2 nm. The genome sequence of this phage was 34, 257 bp and had a GC content of 40...
December 2023: Marine Genomics
https://read.qxmd.com/read/38008528/complete-genome-of-polaribacter-huanghezhanensis-kctc-32516-t-isolated-from-glaciomarine-fjord-sediment-of-svalbard
#14
JOURNAL ARTICLE
Kyuin Hwang, Hanna Choe, Kyung Mo Kim
Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P...
December 2023: Marine Genomics
https://read.qxmd.com/read/37620056/genome-analysis-of-tepidibacter-sp-swir-1-an-anaerobic-endospore-forming-bacterium-isolated-from-a-deep-sea-hydrothermal-vent
#15
JOURNAL ARTICLE
Xue-Gong Li, Jie Dai, Wei-Jia Zhang, Ai-Jun Jiang, Deng-Hui Li, Long-Fei Wu
Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C content and a circular plasmid comprising 38,843 nucleotides with 29.46% G + C content...
October 2023: Marine Genomics
https://read.qxmd.com/read/37620055/complete-genome-of-rossellomorea-sp-da94-an-agarolytic-and-orange-pigmented-bacterium-isolated-from-mangrove-sediment-of-the-south-china-sea
#16
JOURNAL ARTICLE
Qun-Jian Yin, Hong-Zhi Tang, Fang-Chao Zhu, Xin Liu, Yong-Ze Xing, Li-Chang Tang, Xue-Gong Li
Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains...
October 2023: Marine Genomics
https://read.qxmd.com/read/37620054/isolation-and-genome-sequencing-of-a-novel-lytic-pseudoalteromonas-phage-sl20
#17
JOURNAL ARTICLE
Huifang Li, Jie Gao, Shiyun Ma, Rongda Xiao, Xing Zhou, Wanting Feng, Siyu Zhao, Jiaqi Luo, Di Zhang
Phage SL20, a novel lytic Pseudoalteromonas phage, was isolated from the coastal waters of the Yellow Sea, China. The microbiological characterization demonstrated that phage SL20 was relatively stable from 35 to 55 °C and the optimal pH was approximately 6.0. A latent period of approximately 24 min was indicated by a one-step growth curve. The burst size was approximately 12 ± 3 PFU/cell. The genome had a length of 120,295 bp with a G + C content of 35.84%, and predicted 95 ORFs...
October 2023: Marine Genomics
https://read.qxmd.com/read/37620053/complete-genome-sequence-of-pectin-degrading-flavobacteriaceae-bacterium-gsb9
#18
JOURNAL ARTICLE
Binna Lee, Jeong Ah Kim, Yunjon Han, Jae Jun Song, Jong Hyun Choi, Ji Young Kang
Pectic oligosaccharides, which are considered to be potential prebiotics, may be generated by pectin-degrading enzymes. Here, we report the complete genome sequence of the pectin-degrading marine bacterium, Flavobacteriaceae bacterium GSB9, which was isolated from seawater of South Korea. The complete genome sequence revealed that the chromosome was 3,630,376 bp in size, had a G + C content of 36.6 mol%, and was predicted to encode 3100 protein-coding sequences (CDSs), 40 tRNAs, and six 16S-23S-5S rRNAs...
October 2023: Marine Genomics
https://read.qxmd.com/read/37567081/size-and-site-specific-transcriptomic-responses-of-blue-mussel-mytilus-edulis-to-acute-hypoxia
#19
JOURNAL ARTICLE
Stephanie Hall, Denise Méthé, Sarah Stewart-Clark, Fraser Clark
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...
August 9, 2023: Marine Genomics
https://read.qxmd.com/read/37355295/genomic-analysis-of-marinomonas-algicola-sm1966-t-reveals-its-role-in-marine-sulfur-cycling
#20
JOURNAL ARTICLE
Min Zhang, Xiao-Di Wang, Yue Lin, Shu-Yan Wang, Shan Zhang, Jin Cheng, Mei-Ling Sun, Peng Wang, Hui-Hui Fu, Chun-Yang Li, Nan Zhang
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. Marinomonas algicola SM1966T , a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of Ulva pertusa (Chlorophyta) algal sample collected off the coastal areas of Rongcheng, China. Here, we report the complete genome sequence of strain SM1966T and its genomic characteristics to utilize DMSP, which may be produced by Ulva pertusa...
August 2023: Marine Genomics
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