BMC genomic data最新文献

{"title":"Population-resourced species-specific InDel markers for identifying putative interspecific hybrids between Populus euphratica and Populus pruinosa.","authors":"Ya Li, Shanhe Zhang, Wenli Ma, Xinyue Long, Yafen Chen, Zhongshuai Gai","doi":"10.1186/s12863-026-01486-8","DOIUrl":"10.1186/s12863-026-01486-8","url":null,"abstract":"<p><strong>Background: </strong>Populus euphratica and Populus pruinosa represent core germplasm resources of desert riparian forests in northwest China. Accurate discrimination of putative interspecific hybrids between the two species is fundamental to population genetic research of desert poplars. Currently, publicly available and standardized genome-wide InDel marker resources specifically for desert poplars remain scarce. Traditional morphological identification exhibits low accuracy and reliability, and conventional markers (RAPD, AFLP, SSR) have limited repeatability and species specificity, failing to support standardized genotyping. Based on large-scale whole-genome resequencing data, this study developed and validated a set of highly specific and stable InDel markers to provide valuable genomic resources for subsequent genetic research on desert poplars.</p><p><strong>Results: </strong>A total of 56,864 interspecific InDel loci with fragment length differences over 5 bp were screened from 439 P. euphratica and 146 P. pruinosa resequencing accessions, among which 3,417 loci had interspecific allele frequency differences > 0.9. After primer design and native polyacrylamide gel electrophoresis (native-PAGE) validation, 11 universal InDel primer pairs were obtained, and two robust diagnostic markers (P1599-3, P1599-4) were finally verified. Population validation involving 50 P. euphratica, 41 P. pruinosa and 93 morphologically selected putative-hybrid individuals revealed that this dual-marker set could reliably detect biparental banding patterns among tested candidates.</p><p><strong>Conclusion: </strong>The two verified co-dominant InDel markers provide reusable molecular resources for preliminary germplasm authentication and screening of putative hybrids within Populus sect. Turanga. The standardized screening and PAGE genotyping pipeline provided in this study can be transferred to other woody hybrid species, supporting marker-assisted breeding and germplasm conservation of arid poplars.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149027134","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":"Correction: Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest.","authors":"Priscila A Moura, Swee-Peck Quek, Márcio Z Cardoso, Marcus R Kronforst","doi":"10.1186/s12863-026-01457-z","DOIUrl":"10.1186/s12863-026-01457-z","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13525640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148852028","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":"MEFV variant spectrum and exploratory in silico stratification of uncommon variants in 611 individuals tested for suspected familial Mediterranean fever in the Eastern Black Sea region of Türkiye.","authors":"Çağrı Doğan","doi":"10.1186/s12863-026-01481-z","DOIUrl":"10.1186/s12863-026-01481-z","url":null,"abstract":"<p><strong>Background: </strong>Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease, caused by variants in the MEFV gene. Regional MEFV variant spectra differ across Türkiye. We characterised the MEFV variant spectrum in a single-centre series of individuals tested for suspected FMF in the Eastern Black Sea region and explored in silico stratification of uncommon variants. No standardised clinical diagnostic criteria were applied; the study is therefore framed as a molecular variant-spectrum study.</p><p><strong>Methods: </strong>We retrospectively analysed MEFV next-generation sequencing (NGS) reports from 611 consecutive individuals referred with a clinical suspicion of FMF (January 2022-October 2025). Standardised FMF classification criteria (Tel-Hashomer; Eurofever/PRINTO) were not applied; the cohort was defined by referral indication. For each variant, two metrics were reported: the proportion within the detected mutant-allele pool (n/591) and the allele frequency across all tested chromosomes (n/1222; 2 × 611). Uncommon variants were defined as all detected missense variants other than the recognised common FMF alleles (R202Q, M694V, M680I, M694I, V726A, E148Q, P369S, R408Q). Uncommon variants were submitted to the seven-tier framework of Alay (2025) as an exploratory layer supplementary to - not a replacement for - ACMG/AMP classification.</p><p><strong>Results: </strong>At least one variant was detected in 379/611 individuals (62.0%); 591 alleles across 22 distinct missense variants were tabulated. R202Q was the most frequently detected allele in the spectrum (44.0% of detected mutant alleles; 21.3% of all tested chromosomes), exceeding M694V (22.3%; 10.8%). When restricted to high-penetrance exon 10 founder variants (M694V, M680I, M694I, V726A), the pathogenic-allele burden was substantially lower (202 alleles; 16.5% of tested chromosomes). Compound/complex genotypes were present in 25.7% of the cohort (cis/trans phase not determined). Exploratory in silico stratification flagged 7 of 10 evaluable uncommon variants toward likely-pathogenic and 3 toward likely-benign; four variants could not be mapped. A previously unreported substitution, p.Ser179Gly, was detected in one individual and is reported only as a candidate variant of uncertain significance, without pathogenicity inference.</p><p><strong>Conclusions: </strong>In this region, R202Q predominates in the detected MEFV variant spectrum; however, its contested pathogenicity means that spectrum dominance should not be equated with regional clinical or pathogenic-allele burden. The findings describe a molecular variant spectrum, and clinical interpretation is constrained by the absence of phenotype, segregation and standardised diagnostic data. In silico stratification is exploratory and does not replace ACMG/AMP classification.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042256","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":"Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions.","authors":"Gi Uk Hong, Ye Jin Gwak, Yujin Hwang, Ji Young Jung, Hyo Jung Lee","doi":"10.1186/s12863-026-01477-9","DOIUrl":"https://doi.org/10.1186/s12863-026-01477-9","url":null,"abstract":"<p><strong>Objective: </strong>Bacteria respond to iron limitation by activating distinct uptake and siderophore-biosynthesis pathways, and comparative transcriptomics under varying iron availability provide insights into these diverse adaptive mechanisms. Here we describe RNA-seq datasets generated from four freshwater bacterial isolates-Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738-cultured under FeCl₃-treated and untreated conditions. For each strain-condition combination, three biological replicate cultures were prepared, their RNA was pooled, and a single sequencing library was constructed.</p><p><strong>Data description: </strong>The dataset comprises eight paired-end libraries (16 FASTQ files) generated in 2024 and 2025, totaling 349,853,404 processed reads. Raw sequence data are openly available in the NCBI Sequence Read Archive under SRA study accession SRP695241 (BioProject PRJNA1456794; SRR38280322-SRR38280329; BioSamples SAMN57450602-SAMN57450609). Read alignment rates were 78.59% and 71.98% for Pseudomonas sp. FBCC-B13192, 92.30% and 89.11% for Herbaspirillum sp. B12834, 89.29% and 89.23% for Pantoea sp. FBCC-B5559, and 34.75% and 21.39% for Micrococcus sp. FBCC-B5738 under FeCl₃-treated and untreated conditions, respectively. Quality-control summaries, sample metadata, and figure files are listed in Table 1; these will be released through figshare. The dataset enables comparative analyses of bacterial iron-acquisition responses and supports reanalysis with future transcriptome workflows.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13474768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762503","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 inactivated animal vaccine bacteria strains in South Korea.","authors":"Yeonkyeong Lee, Jin-Ju Nah, Su-Min Go, Hyun-Ok Ku, Il Jang","doi":"10.1186/s12863-026-01475-x","DOIUrl":"10.1186/s12863-026-01475-x","url":null,"abstract":"<p><strong>Objectives: </strong>Production of high-quality biological products depends on the careful selection and consistent management of seed strains. In this study, we generated complete genome sequences of bacterial strains employed in inactivated animal vaccines in South Korea and comprehensively examined their gene annotations. The genome data thus obtained provide a solid basis for confirming, at the strain level, whether manufacturers are using the same seed strains over time. In addition, these data offer a useful reference resource to support stable large-scale production and quality control of biological products.</p><p><strong>Data description: </strong>The complete genomes of eleven bacterial strains employed for inactivated vaccine production were generated and annotated. A hybrid assembly workflow combining Illumina short reads (NovaSeq 6000) with Oxford Nanopore long reads (MinION) produced high-quality, gap-free genomes for all strains, with genome sizes ranging from 2.28 Mb to 5.35 Mb. The strains comprised Pasteurella multocida (D, 3A, A), Actinobacillus pleuropneumoniae (2 and 5), Glaesserella parasuis 4, Mannheimia haemolytica KO, Avibacterium paragallinarum C, and three Escherichia coli strains (F41, YC21-F17, K99S). All assemblies exhibited high completeness (>99%) and minimal contamination (<1%), ensuring reliable downstream genomic characterization.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708698","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 Marinobacterium marisflavi strain IMCC4074 isolated from coastal seawater.","authors":"Meora Rajeev, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho","doi":"10.1186/s12863-026-01454-2","DOIUrl":"10.1186/s12863-026-01454-2","url":null,"abstract":"<p><strong>Objectives: </strong>Members of the genus Marinobacterium are widely distributed in marine environments and contribute to diverse ecological processes; however, genomic information for several species remains limited. In this study, we report the complete genome sequence of Marinobacterium marisflavi strain IMCC4074ᵀ, originally isolated from coastal seawater of the Yellow Sea, to provide insights into its genomic features, metabolic potential, and environmental adaptation.</p><p><strong>Data description: </strong>The genome of strain IMCC4074ᵀ was sequenced using a combination of short- and long-read sequencing approaches and assembled into a single circular chromosome of 3,091,487 bp with a G + C content of 52.45%. Genome annotation revealed 2,974 protein-coding sequences, 15 rRNA genes, and 60 tRNA genes. Phylogenomic analyses confirmed its taxonomic placement within the genus Marinobacterium, while comparative genomic analysis revealed sufficient divergence (ANI ≤ 95%) from previously described species within the genus, supporting its distinction at the species level and representing the first genome report for this species. The availability of the complete genome provides a resource for understanding the potential ecological roles and adaptive strategies of M. marisflavi in marine ecosystems.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148690369","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":"De novo genome assembly of the deepwater rice (Oryza sativa) cultivar Pin Gaew 56.","authors":"Hoon Je Seong, Sung Un Huh, Tae-Ho Lee, Dongsu Choi","doi":"10.1186/s12863-026-01476-w","DOIUrl":"10.1186/s12863-026-01476-w","url":null,"abstract":"<p><strong>Objectives: </strong>We present the de novo whole-genome assembly of a deepwater rice variety (Oryza sativa cv. Pin Gaew 56). Although the submergence escape response is a vital survival strategy in deepwater rice, current reference genomes lack sufficient genetic information to fully understand the molecular mechanisms behind this complex physiological process. Pin Gaew 56 (PG56) is a well-studied genetic resource with extensively documented physiological and molecular traits related to internode elongation under partial submergence. This study provides a cultivar-specific genomic resource for PG56 that can support further investigation of the genetic basis of the submergence escape response.</p><p><strong>Data description: </strong>A de novo whole-genome assembly of the deepwater rice cultivar PG56 was generated to support genomic studies of the submergence escape response. The final assembly has a total length of 407.7 Mb, comprising 138 scaffolds with an N50 of 32.5 Mb. Genome completeness assessed by BUSCO showed 94.5% complete BUSCOs, and continuity in LTR-rich regions was supported by an LTR Assembly Index of 28.2. Assembly quality was further supported by k-mer-based quality assessment and whole-genome synteny alignment against the MH63 reference genome. Together, these data provide a useful genomic resource for investigating the genetic mechanisms underlying internode elongation and flooding adaptation in deepwater rice.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708637","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":"The complete organelle genomes of Crateva unilocularis (Capparaceae).","authors":"Zhen-Yu Lyu, Lin Yang, Shi-Kang Shen","doi":"10.1186/s12863-026-01472-0","DOIUrl":"10.1186/s12863-026-01472-0","url":null,"abstract":"<p><strong>Objective: </strong>Crateva unilocularis is a widely consumed woody vegetable in the family Capparaceae. This study aimed to generate and comprehensively characterize the first complete mitochondrial genome of C. unilocularis using PacBio HiFi long-read sequencing, elucidating its structural organization and gene content. We also report the complete chloroplast genome for this accession. Together, these organelle genome resources provide a foundation for downstream studies on phylogeny, genome architecture, and adaptive evolution in C. unilocularis and related taxa.</p><p><strong>Data description: </strong>The chloroplast genome length of C. unilocularis is 156,525 bp, harboring 78 unique protein-coding genes (PCGs), 28 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). In addition, the assembly graph supports three circular mitochondrial molecules with a combined length of 566,203 bp, and junction-spanning HiFi reads validate the assembled configurations. Annotation identified 59 genes in total, including 37 PCGs, 19 tRNAs, and three rRNAs. The assembled and annotated organelle genomes represent key reference sequences for C. unilocularis within Capparaceae and will facilitate future comparative and functional genomic analyses.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498408","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 assembly of hyper citric acid-producing Aspergillus niger mutant strain developed through gamma radiation bombardment.","authors":"Ambreen Latif, Hazrat Ali, Muhammad Salman Haider, Muhammad Bilal Khan Niazi, Noor Hassan, Asad Ali","doi":"10.1186/s12863-026-01467-x","DOIUrl":"10.1186/s12863-026-01467-x","url":null,"abstract":"<p><strong>Objectives: </strong>Aspergillus niger is a renowned filamentous fungus with extensive industrial and biotechnological applications. A. niger is widely used to produce diverse organic acids, enzymes, and other value-added metabolites. Although strain-specific metabolic capabilities have been widely applied in industry, the genomic foundations of these capabilities have not yet been fully characterized. Here, we have described the isolation and provided the draft genome sequence of A. niger strain AN-L103_M1 to further study the genetic determinants of primary and secondary metabolism, given its metabolic versatility and great potential in biotechnology. This A. niger strain was developed through gamma radiation bombardment, and subsequently, all the mutants were screened through various steps for hyperproduction of citric acid. This genome sequence provided valuable information for further functional genomics and strain-improvement research.</p><p><strong>Data description: </strong>The A. niger strain was obtained through gamma radiation bombardment. After gamma radiation bombardment of the A. niger culture, it was subjected to various screening steps to achieve hyperproduction of citric acid. These experiments were performed in the Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. The mycotoxin production potential of this mutant strain was assessed using LC-MS analysis, which detected no mycotoxins.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474348","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":"Molecular identification of some wild macrofungi from Southeastern Nigeria.","authors":"Chidera Valentine Odo, Eugene Obashi Ojua, Akpevwoghene Agbatutu, Chiemeka Nwakaego Onaebi, Ololade Titilayo Oyediran, Uchenna Oliver Egedigwe, Obinna Victor James, Maria Chinwendu Anyadike-Ezeonwumelu, Kingsley Chinedu Ubochi, Musibau Emmanuel Momoh, Ngozi Eucheria Abu","doi":"10.1186/s12863-026-01470-2","DOIUrl":"10.1186/s12863-026-01470-2","url":null,"abstract":"<p><p>Mushrooms are grossly under exploited and efforts to domesticate them are not yielding enough results as over 95% of mushrooms consumed in Africa and most parts of the world are still collected from the wild. However, the utility and commercialization of wild mushrooms has been hampered by incorrect morphological identifications. Molecular markers, including the internal transcribed spacer (ITS) region, have proven to be efficient in mushroom diversity studies. This research aimed to investigate the diversity of wild mushrooms indigenous to southeast Nigeria. Fifty (50) samples of wild growing mushrooms were collected using opportunistic sampling method in 5 states of the region. Zymo Research Quick-DNA Plant/Seed Miniprep kit was used for DNA extraction, the ITS region was amplified using PCR and subsequently sequenced with Sanger sequencing technology. BLASTn search in Genbank databases were conducted to determine the identity of the sampled mushrooms. Genomic DNA was successfully extracted and amplified, although with varying band quality. Forty-one (41) out of the 50 mushroom samples were successfully sequenced and identified. The identified mushroom species were classified into 11 families with family Polyporaceae (13), Agaricaceae (9), Omphatotaceae (7) and Ganodermataceae (4), topping the list. Trametes (7) and Lentinus (6) were the most abundant genera followed by Neonothopanus (5), and Ganoderma (4). Barcode marker (ITS region) was effective in identifying the wild mushrooms of Southeastern Nigeria.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474359","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}