Journal of Genomics最新文献_第2页

Complete Genome Sequence of Annamia dubia, filamentous colony-making Chroococcales with the analysis of FraC gene influencing filament integrity. 姬松茸（Annamia dubia）的完整基因组序列（丝状菌落制造的 Chroococcales），以及影响菌丝完整性的 FraC 基因分析。

Journal of Genomics Pub Date : 2024-01-01 DOI: 10.7150/jgen.87678

Akihiro Tuji, Eri Ogiso-Tanaka, Haruyo Yamaguchi

{"title":"Complete Genome Sequence of Annamia dubia, filamentous colony-making Chroococcales with the analysis of FraC gene influencing filament integrity.","authors":"Akihiro Tuji, Eri Ogiso-Tanaka, Haruyo Yamaguchi","doi":"10.7150/jgen.87678","DOIUrl":"10.7150/jgen.87678","url":null,"abstract":"The complete genome of Annamia dubia was sequenced. The genome size is 4.02 Mbp, including 3886286 bp circular chromosome and four circular plasmids (31516, 42453, 38085 and 24903 bp). It included 3718 protein-coding sequences, 45 tRNA genes, three sets of rRNA genes, a microcystin biosynthesis gene cluster and six CRISPR (clustered regularly interspaced short palindromic repeat). Annamia is the only one genus in the Chroococcales that makes filamentous colonies. FraC and FraG were identified in the genome. These genes are required for the integrity of cell junctions and influencing filament integrity and are thought to be related to colony formation. These genes are first reported from Chroococcales, and may play a significant role in the colony formation of this species. In the phylogenetic tree of the FraC gene, A. dubia was located in the basal position of Oscillatoriales. The GC ratio of FraC gene of A. dubia is very low from the genome and the FraC gene of Microcoleaceae. The presence of these genes in the basal region and the low GC ratio suggests that the FraC gene in this species was introduced by horizontal gene transfer. Since the filamentous colony is a fundamental and important taxonomic feature for the classification of cyanobacteria, the possibility of horizontal transmission of genes involved in filamentous cyanobacterial colonies is an important discovery for the classification of cyanobacteria.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10751749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole genome sequencing of Streptomyces antnestii sp. nov. with a potency to become an industrial strain. 对有可能成为工业菌株的 Streptomyces antnestii sp.

Journal of Genomics Pub Date : 2024-01-01 DOI: 10.7150/jgen.87156

Saroja Chhettri, Joseph Sevigny, Céline Pesce, Indrani Sarkar, W Kelley Thomas, Imen Nouioui, Gargi Sen, Louis S Tisa, Arnab Sen

{"title":"Whole genome sequencing of Streptomyces antnestii sp. nov. with a potency to become an industrial strain.","authors":"Saroja Chhettri, Joseph Sevigny, Céline Pesce, Indrani Sarkar, W Kelley Thomas, Imen Nouioui, Gargi Sen, Louis S Tisa, Arnab Sen","doi":"10.7150/jgen.87156","DOIUrl":"10.7150/jgen.87156","url":null,"abstract":"Streptomyces Strain San01 is isolated from the soil of ant-nest found in the tea estate of Darjeeling, India. The morphology, biochemical, as well as the molecular characteristics, proved that San01 belonged to the genus Streptomyces. The average nucleotide identity (ANI) value between the genome sequence of the studied strain and its closest phylogenetic neighbors were very low and also could be distinguished from its closest neighbour with broad range of phenotypic data. The draft genome sequence of isolate San01 (NZ_RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasize the biotechnological potential of this isolate.Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp. nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"12 ","pages":"6-13"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10751750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139074279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reference Genome Resource for the Citrus Pathogen Phytophthora citrophthora. 柑橘病原体 Phytophthora citrophthora 的参考基因组资源。

Journal of Genomics Pub Date : 2024-01-01 DOI: 10.7150/jgen.89324

Heike Möller, Beatrix Coetzee, Jan van Niekerk, Lindy Joy Rose

引用次数: 0

Permanent draft genome sequence of Bradyrhizobium vignae, strain ISRA 400, an elite nitrogen-fixing bacterium, isolated from the groundnut growing area in Senegal. 从塞内加尔花生种植区分离的优质固氮细菌慢生根瘤菌ISRA 400菌株的永久基因组序列草案。

Journal of Genomics Pub Date : 2023-11-01 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.88302

Diariatou Niang, Abdellatif Gueddou, Nogaye Niang, Darius Nzepang, Aissatou Sambou, Adama Diouf, Arlette Z Zaiya, Maimouna Cissoko, Djamel Gully, Joel-Romaric Nguepjop, Sergio Svistoonoff, Daniel Fonceka, Valérie Hocher, Diégane Diouf, Saliou Fall, Louis S Tisa

{"title":"Permanent draft genome sequence of Bradyrhizobium vignae, strain ISRA 400, an elite nitrogen-fixing bacterium, isolated from the groundnut growing area in Senegal.","authors":"Diariatou Niang, Abdellatif Gueddou, Nogaye Niang, Darius Nzepang, Aissatou Sambou, Adama Diouf, Arlette Z Zaiya, Maimouna Cissoko, Djamel Gully, Joel-Romaric Nguepjop, Sergio Svistoonoff, Daniel Fonceka, Valérie Hocher, Diégane Diouf, Saliou Fall, Louis S Tisa","doi":"10.7150/jgen.88302","DOIUrl":"https://doi.org/10.7150/jgen.88302","url":null,"abstract":"A new Bradyrhizobium vignae strain called ISRA400 was isolated from groundnut (Arachis hypogaea L.) root nodules obtained by trapping the bacteria from soil samples collected in the Senegalese groundnut basin. In this study, we present the draft genome sequence of this strain ISRA400, which spans approximatively 7.9 Mbp and exhibits a G+C content of 63.4%. The genome analysis revealed the presence of 48 tRNA genes and one rRNA operon (16S, 23S, and 5S). The nodulation test revealed that this strain ISRA400 significantly improves the nodulation parameters and chlorophyll content of the Arachis hypogaea variety Fleur11. These findings suggest the potential of Bradyrhizobium vignae strain ISRA400 as an effective symbiotic partner for improving the growth and productivity of groundnut crop.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"52-57"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71424077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation, draft genome sequence, and identification of Paenibacillus glycanilyticus subsp. hiroshimensis CCS26. 帕尼巴菌多糖裂解亚种的分离、基因组序列草案和鉴定。广岛CCS26。

Journal of Genomics Pub Date : 2023-09-25 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.87229

Hironaga Akita, Yoshiki Shinto, Zen-Ichiro Kimura

引用次数: 0

Isolation and draft genome sequence of Paenibacillus sp. CCS19. Paenibacillus sp.CCS19。

Journal of Genomics Pub Date : 2023-09-11 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.87228

Hironaga Akita, Yoshiki Shinto, Zen-Ichiro Kimura

引用次数: 0

Genomic analysis of Chlamydia psittaci from a multistate zoonotic outbreak in two chicken processing plants. 来自两个鸡肉加工厂的多州人畜共患疫情的鹦鹉热衣原体基因组分析。

Journal of Genomics Pub Date : 2023-08-19 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.86558

Bernard J Wolff, Jessica L Waller, Alvaro J Benitez, Anna Gaines, Andrew B Conley, Lavanya Rishishwar, Aroon T Chande, Shatavia S Morrison, I King Jordan, Maureen H Diaz, Jonas M Winchell

引用次数: 0

Complete Genome Sequence of Floricoccus penangensis ML061-4 Isolated from Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.]. 从阿萨姆邦茶叶中分离的penangensis Floricoccus ML061-4的全基因组序列。

Journal of Genomics Pub Date : 2023-07-16 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.83521

Patthanasak Rungsirivanich, Elvina Parlindungan, Jennifer Mahony, Ian O'Neill, Brian McDonnell, Francesca Bottacini, Witsanu Supandee, Narumol Thongwai, Douwe van Sinderen

引用次数: 0

Draft Genome Sequences of Synechococcus sp. strains CCAP1479/9, CCAP1479/10, CCAP1479/13, CCY0621, and CCY9618: Five Freshwater Syn/Pro Clade Picocyanobacteria. 聚球藻属菌株CCAP1479/9、CCAP1479/10、CCAP1179/13、CCY0621和CCY9618的基因组序列草案：五种淡水聚/前支微微蓝细菌。

Journal of Genomics Pub Date : 2023-04-25 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.81013

Elliot Druce, Michele Grego, Henk Bolhuis, Penny J Johnes, Patricia Sánchez-Baracaldo

{"title":"Draft Genome Sequences of Synechococcus sp. strains CCAP1479/9, CCAP1479/10, CCAP1479/13, CCY0621, and CCY9618: Five Freshwater Syn/Pro Clade Picocyanobacteria.","authors":"Elliot Druce, Michele Grego, Henk Bolhuis, Penny J Johnes, Patricia Sánchez-Baracaldo","doi":"10.7150/jgen.81013","DOIUrl":"10.7150/jgen.81013","url":null,"abstract":"Picocyanobacteria are essential primary producers in freshwaters yet little is known about their genomic diversity and ecological niches. We report here five draft genomes of freshwater picocyanobacteria: Synechococcus sp. CCAP1479/9, Synechococcus sp. CCAP1479/10, and Synechococcus sp. CCAP1479/13 isolated from Lake Windermere in the Lake District, UK; and Synechococcus sp. CCY0621 and Synechococcus sp. CCY9618 isolated from lakes in The Netherlands. Phylogenetic analysis reveals all five strains belonging to sub-cluster 5.2 of the Synechococcus and Prochlorococcus clade of Cyanobacteria. These five strains are divergent from Synechococcus elongatus, an often-used model for freshwater Synechococcus. Functional annotation revealed significant differences in the number of genes involved in the transport and metabolism of several macro-molecules between freshwater picocyanobacteria from sub-cluster 5.2 and Synechococcus elongatus, including amino acids, lipids, and carbohydrates. Comparative genomic analysis identified further differences in the presence of photosynthesis-associated proteins while gene neighbourhood comparisons revealed alternative structures of the nitrate assimilation operon nirA.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"26-36"},"PeriodicalIF":0.0,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10161378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9423576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland. 从波兰喀尔巴阡山前陆的盐水中分离的嗜盐古菌菌株的基因组草案。

Journal of Genomics Pub Date : 2023-04-10 eCollection Date: 2023-01-01 DOI: 10.7150/jgen.82493

Jakub Lach, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek

{"title":"Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland.","authors":"Jakub Lach, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek","doi":"10.7150/jgen.82493","DOIUrl":"10.7150/jgen.82493","url":null,"abstract":"Halophilic Archaea are a unique group of microorganisms living in saline environments. They constitute a complex group whose biodiversity has not been thoroughly studied. Here, we report three draft genomes of halophilic Archaea isolated from brines, representing the genera of Halorubrum, Halopenitus, and Haloarcula. Two of these strains, Boch-26 and POP-27, were identified as members of the genera Halorubrum and Halopenitus, respectively. However, they could not be assigned to any known species because of the excessive difference in genome sequences between these strains and any other described genomes. In contrast, the third strain, Boch-26, was identified as Haloarcula hispanica. Genome lengths of these isolates ranged from 2.7 Mbp to 3.0 Mbp, and GC content was in the 63.77%-68.77% range. Moreover, functional analysis revealed biosynthetic gene clusters (BGCs) related to terpenes production in all analysed genomes and one BGC for RRE (RiPP recognition element)-dependent RiPP (post-translationally modified peptides) biosynthesis. Moreover, the obtained results enhanced the knowledge about the salt mines microbiota biodiversity as a poorly explored environment so far.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"11 ","pages":"20-25"},"PeriodicalIF":0.0,"publicationDate":"2023-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10093198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9418856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0