BMC genomic data最新文献

{"title":"Draft genome of the Cuban Painted Landsnail Polymita picta, International Mollusc of the year 2022.","authors":"Bernardo Reyes-Tur, Zeyuan Chen, Mario Juan Gordillo-Pérez, Alexander Ben Hamadou, Charlotte Gerheim, Carola Greve, Julia D Sigwart","doi":"10.1186/s12863-025-01356-9","DOIUrl":"10.1186/s12863-025-01356-9","url":null,"abstract":"<p><strong>Objective: </strong>The Cuban Painted Landsnail is an iconic endemic tree snail species with distinctive colourful shells used in traditional handicrafts. This species won the International Mollusc of the Year 2022 competition in an open public vote. As the competition prize, we have assembled the draft genome of this species.</p><p><strong>Data description: </strong>Genomic DNA from Polymita picta (Born, 1778) was sequenced using PacBio HiFi sequencing with a yield of 5.3 million reads (41.4 Gb) and an N50 of 8.1 Kb. The genome size of P. picta was estimated to be 2.9 Gb, and the final assembly was 1.85 Gb, with a total of 22,619 contigs and a contig N50 of 124.2 Kb. BUSCO analysis of the genome assembly indicated a genome completeness of 88.4%, with 7% complete duplicated BUSCOs in metazoa_odb10. The draft genome will be a valuable resource for work on the endangered Cuban Painted Landsnail including monitoring genetic diversity and establishing captive breeding for conservation.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"63"},"PeriodicalIF":2.5,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994581","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}

{"title":"High-quality genome assembly and annotation of live animal vaccine bacteria strains in South Korea.","authors":"Yeonkyeong Lee, Jin-Ju Nah, Hyun-Ok Ku, Il Jang","doi":"10.1186/s12863-025-01357-8","DOIUrl":"10.1186/s12863-025-01357-8","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"62"},"PeriodicalIF":2.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12406338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980732","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}

{"title":"Complete genome sequence of the probiotic candidate strain Lacticaseibacillus rhamnosus B3421 isolated from Panax ginseng C. A. Meyer in South Korea.","authors":"Gwi-Deuk Jin, Ho-Youn Kim, Eun Bae Kim, Bokyung Lee","doi":"10.1186/s12863-025-01344-z","DOIUrl":"https://doi.org/10.1186/s12863-025-01344-z","url":null,"abstract":"<p><strong>Objectives: </strong>Lacticaseibacillus rhamnosus is a widely recognized probiotic bacteria with therapeutic applications in human and animal health. The L. rhamnosus B3421 strain, isolated from Panax ginseng, has been reported to be associated with antioxidant and anti-inflammatory properties, supporting its functional potential. We sequenced and analyzed the genome of L. rhamnosus B3421 to evaluate its probiotic potential for human healthcare and animal applications, focusing on genomic features related to safety and functionality.</p><p><strong>Data description: </strong>In this study, we isolated L. rhamnosus B3421 from Panax ginseng C. A. Meyer (Ginseng) and performed whole-genome sequencing. The genome of L. rhamnosus B3421 consists of 3,000,051 base pairs (bp) with a guanine + cytosine (G + C) content of 46.70%. It encodes 59 transfer RNAs, 15 ribosomal RNAs, and 2,807 coding sequences (CDSs). Of these CDSs, 99.13% (2,758 proteins) were assigned to functional categories in the Clusters of Orthologous Group (COGs) classification system, while 49 proteins remained uncharacterized. Our genome analysis identified no antibiotic resistance (ABR) or antimicrobial resistance (AMR) genes, indicating that L. rhamnosus B3421 is a safe probiotic bacterium with minimal risk of contributing to the horizontal transfer of antibiotic resistance within the gut microbiome. Additionally, the genome contains genes associated with the ggmotif (PF10439), Enterocin X chain beta, and Carnocin CP52, as identified through BAGEL4 analysis, along with 24 other genes related to reductase or peroxidase activities. These genes may confer competitive advantages against pathogenic bacteria and oxidative stress. Our findings highlight the probiotic potential of L. rhamnosus B3421 and its prospective applications in promoting human and animal health.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"61"},"PeriodicalIF":2.5,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980728","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}

{"title":"Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.","authors":"Olubukola Oluranti Babalola, Florence Oluwayemisi Ogundeji, Akinlolu Olalekan Akanmu","doi":"10.1186/s12863-025-01351-0","DOIUrl":"https://doi.org/10.1186/s12863-025-01351-0","url":null,"abstract":"<p><strong>Objectives: </strong>This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.</p><p><strong>Data description: </strong>The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"60"},"PeriodicalIF":2.5,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12376418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980661","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}

{"title":"Oar_Finn: the genome assembly and annotation of an exceptionally fertile Finnsheep (Ovis aries) Ewe.","authors":"Juha Kantanen, Melak Weldenegodguad, Kisun Pokharel","doi":"10.1186/s12863-025-01354-x","DOIUrl":"10.1186/s12863-025-01354-x","url":null,"abstract":"<p><strong>Objectives: </strong>Finnsheep, a highly prolific breed of sheep, has been globally exported for improving fertility traits of many sheep breeds. Published genomic studies of Finnsheep have been based on Texel and Rambouillet reference genomes, which may not capture its unique genetic features. Our main objective was to generate a high-quality Finnsheep genome assembly and its annotation that could serve as a breed-specific reference for studying fertility and adaptation in Finnsheep and other short-tailed northern European sheep breeds.</p><p><strong>Data description: </strong>We generated a 2.53 Gb assembly using PacBio HiFi long-reads and Hi-C sequencing from a highly fertile Finnsheep ewe. The assembly, scaffolded with Hi-C data has a contig N50 of 35.5 Mb and scaffold N50 of 100.6 Mb. Gene annotation identified 42,533 genes spanning 46.5 Mb of coding region. BUSCO completeness for the assembly and annotation was 94.9% and 84.3%, respectively. This data, including raw reads, assembly, and annotations supports genomic studies of Finnsheep and other prolific breeds of sheep that are particularly adapted to northern European environments.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"59"},"PeriodicalIF":2.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877038","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}

{"title":"Complete genome sequence of the halophilic archaeon Haloferax volcanii PC0224, isolated from a solar saltern in Thailand.","authors":"Manassanan Phatcharaharikarn, Pattarawan Ruangsuj, Thunwarat Songngamsuk, Parweenuch Santaweesuk, Marut Tangwattanachuleeporn, Kanokporn Srisucharitpanit, Prapimpun Wongchitrat, Montri Yasawong","doi":"10.1186/s12863-025-01353-y","DOIUrl":"10.1186/s12863-025-01353-y","url":null,"abstract":"<p><strong>Objectives: </strong>Haloferax volcanii is an extreme halophile belonging to the Haloferacaceae family that thrives in hypersaline environments. This study presents the complete genome sequence of the H. volcanii strain PC0224 isolated from a Thai solar saltern. Genomic data will enhance our understanding of circadian rhythm mechanisms and their evolutionary significance in extremophilic archaea.</p><p><strong>Data description: </strong>The H. volcanii PC0224 genome comprises four circular sequences containing 3,773,977 bp and 66.16% GC content. Sequenced using Illumina and PacBio technologies and assembled with Hybracter, the genome contained 3,731 CDS, 6 rRNAs, 54 tRNAs, 2 ncRNAs, and 4 CRISPR arrays. This dataset enables the investigation of circadian rhythm regulatory systems and comparative genomic studies of temporal adaptation mechanisms in extremophilic archaea.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"58"},"PeriodicalIF":2.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877036","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}

{"title":"Development of a composite core collection from 5,856 Sesame accessions being conserved in the Indian National Genebank.","authors":"Pradeep Ruperao, Kapil Tiwari, Vandana Rai, Rashmi Yadav, Mahalingam Angamuthu, Anuj Kumar Singh, Bhemji P Galvadiya, Anshuman Shah, Nitin Gadol, Ajay Kumar, Rajkumar Subramani, Harinder Vishwakarma, Pradheep Kanakasabapathi, Senthilraja Govindasamy, Rasna Maurya, Tamanna Batra, Aravind Jayaraman, Senthil Ramachandran, Abhishek Rathore, Kuldeep Singh, Rakesh Singh, Sanjay Kalia, Ulavappa B Angadi, Sean Mayes, Gyanendra Pratap Singh, Parimalan Rangan","doi":"10.1186/s12863-025-01347-w","DOIUrl":"10.1186/s12863-025-01347-w","url":null,"abstract":"<p><strong>Objectives: </strong>A composite core collection (CCC) in sesame (Sesamum indicum L.) will help utilize genetic resources efficiently. This study reports, using genomics tools, a representative minimal set (CCC) that capture maximal genetic diversity from a set of 5,856 sesame accessions being conserved at the National Genebank (NGB) of the ICAR-NBPGR. The CCC will serve as a valuable resource for researchers and breeders to facilitate sesame improvement for traits such as yield, disease resistance, stress resilience, and nutritional content. Ultimately, this work contributes to the broader goal of improving sesame for an ever-increasing demand for vegetable oil, to meet our food security challenges.</p><p><strong>Data description: </strong>This study presents ddRAD-seq data for a total of 5,856 sesame accessions that includes 2,496 accessions (a subset of 5,856 accessions) that was reported by us recently. Using next-generation sequencing (NGS) short-reads over 2.16 Terabases of sequence data were generated, with each sample averaging 1.2 million reads. The study identifies a set of 1,768 sesame accessions as the CCC that captures maximal diversity, genotypic and phenotypic. This will aid researchers in trait discovery, association studies, pre-breeding, and parental selection for complex traits viz., yield, disease resistance, stress resilience, and other economically important traits.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"57"},"PeriodicalIF":2.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12363036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877037","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}

{"title":"Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.","authors":"Anna Baborski, Stefanie A Barth, Elke Martina Jung, Frank Bloos, Jürgen Rödel, Bettina Löffler, Michael Bauer, Anne Busch","doi":"10.1186/s12863-025-01346-x","DOIUrl":"10.1186/s12863-025-01346-x","url":null,"abstract":"<p><p>Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"56"},"PeriodicalIF":2.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12345040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838713","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}

{"title":"Draft genome sequence and annotation of the enfumafungin producing fungus Hormonema carpetanum ATCC 74360.","authors":"Haodong Chen, Junyi Wang, Songbai Yang, Jiawei Tang, Wen Tang, Shaoxin Chen","doi":"10.1186/s12863-025-01348-9","DOIUrl":"10.1186/s12863-025-01348-9","url":null,"abstract":"<p><strong>Objectives: </strong>Plant endophytic fungusHormonema carpetanum is the only organism known to produce enfumafungin to date. Enfumafungin is a fernane-type triterpenoid glycoside compound with broad-spectrum antifungal activity, and this leading compound has been developed to antifungal agent ibrexafungerp approved by Food and Drug Administration (FDA). Here we report the first de novo assembled and annotated whole-genome sequence of H. carpetanum ATCC 74360, the original enfumafungin producing strain from the American Type Culture Collection (ATCC).</p><p><strong>Data description: </strong>We sequenced the genome of H. carpetanum ATCC 74360 through a hybrid sequencing strategy combining Illumina NovaSeq X Plus short-read and PacBio Sequel IIe long-read technologies. Data from the two platforms were combined and the de novo assembly estimated a 32.93 Mbp genome divided into 16 contigs with a GC content of 49.85%. Genome annotation identified 10,433 genes, 253 tRNAs, and 62 rRNAs. antiSMASH predicted biosynthesis gene cluster (BGC) of secondary metabolite, including enfumafungin BGC. This genome and related data files presented here will provide a foundation for further gene editing of this important antibiotic-producing microorganism.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"55"},"PeriodicalIF":2.5,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12333168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144805400","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}

{"title":"Unveiling the Allium ampeloprasum rhizosphere microbiome and its functional dataset under different fertilization systems.","authors":"Olubukola Oluranti Babalola, Oluwaseun Emmanuel Shittu, Ben Jesuorsemwen Enagbonma","doi":"10.1186/s12863-025-01349-8","DOIUrl":"10.1186/s12863-025-01349-8","url":null,"abstract":"<p><strong>Objectives: </strong>Leek (Allium ampeloprasum) is a nutritious vegetable popularly cultivated in South Africa and most regions of the world. It is generally recognised as a source of vitamins and vegetables. Nevertheless, little is known about its rhizosphere microbiome and its microbial functional dataset under various fertilization systems. Therefore, this study intended to unveil the rhizosphere microbiome of Allium ampeloprasum and their functional datasets through shotgun metagenomics sequencing analysis.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"54"},"PeriodicalIF":2.5,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796273","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}