BMC genomic data最新文献

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Correction: Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest. 更正:濒危栖息地拟斑蝶的比较种群遗传学;巴西的大西洋森林。
IF 2.5
BMC genomic data Pub Date : 2026-08-28 DOI: 10.1186/s12863-026-01457-z
Priscila A Moura, Swee-Peck Quek, Márcio Z Cardoso, Marcus R Kronforst
{"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}
引用次数: 0
Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions. 在富铁和限铁条件下生长的四种淡水细菌分离株转录组数据集。
IF 2.5
BMC genomic data Pub Date : 2026-08-06 DOI: 10.1186/s12863-026-01477-9
Gi Uk Hong, Ye Jin Gwak, Yujin Hwang, Ji Young Jung, Hyo Jung Lee
{"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 FeCl<sub>3</sub>-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 FeCl<sub>3</sub>-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}
引用次数: 0
High-quality genome assembly and annotation of inactivated animal vaccine bacteria strains in South Korea. 韩国灭活动物疫苗菌株的高质量基因组组装和注释。
IF 2.5
BMC genomic data Pub Date : 2026-08-05 DOI: 10.1186/s12863-026-01475-x
Yeonkyeong Lee, Jin-Ju Nah, Su-Min Go, Hyun-Ok Ku, Il Jang
{"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}
引用次数: 0
Complete genome sequence of Marinobacterium marisflavi strain IMCC4074 isolated from coastal seawater. 沿海海水marisflavi Marinobacterium IMCC4074的全基因组序列。
IF 2.5
BMC genomic data Pub Date : 2026-08-05 DOI: 10.1186/s12863-026-01454-2
Meora Rajeev, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
{"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}
引用次数: 0
De novo genome assembly of the deepwater rice (Oryza sativa) cultivar Pin Gaew 56. 深海水稻品种品高56的基因组组装。
IF 2.5
BMC genomic data Pub Date : 2026-08-05 DOI: 10.1186/s12863-026-01476-w
Hoon Je Seong, Sung Un Huh, Tae-Ho Lee, Dongsu Choi
{"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}
引用次数: 0
The complete organelle genomes of Crateva unilocularis (Capparaceae). 龙舌兰(Capparaceae)的细胞器全基因组。
IF 2.5
BMC genomic data Pub Date : 2026-07-19 DOI: 10.1186/s12863-026-01472-0
Zhen-Yu Lyu, Lin Yang, Shi-Kang Shen
{"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":"https://doi.org/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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Draft genome assembly of hyper citric acid-producing Aspergillus niger mutant strain developed through gamma radiation bombardment. 射线轰击培养的高柠檬酸产黑曲霉突变株基因组组装草图。
IF 2.5
BMC genomic data Pub Date : 2026-07-17 DOI: 10.1186/s12863-026-01467-x
Ambreen Latif, Hazrat Ali, Muhammad Salman Haider, Muhammad Bilal Khan Niazi, Noor Hassan, Asad Ali
{"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":"https://doi.org/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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular identification of some wild macrofungi from Southeastern Nigeria. 尼日利亚东南部几种野生大型真菌的分子鉴定。
IF 2.5
BMC genomic data Pub Date : 2026-07-17 DOI: 10.1186/s12863-026-01470-2
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
{"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":"https://doi.org/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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 Lacticaseibacillus rhamnosus B34-0-2 isolated from Panax ginseng in South Korea. 韩国人参中鼠李糖乳杆菌B34-0-2的全基因组序列。
IF 2.5
BMC genomic data Pub Date : 2026-07-14 DOI: 10.1186/s12863-026-01458-y
Sieun Kim, Ye-Rim Choi, Eun Bae Kim, Bokyung Lee
{"title":"Complete genome sequence of Lacticaseibacillus rhamnosus B34-0-2 isolated from Panax ginseng in South Korea.","authors":"Sieun Kim, Ye-Rim Choi, Eun Bae Kim, Bokyung Lee","doi":"10.1186/s12863-026-01458-y","DOIUrl":"https://doi.org/10.1186/s12863-026-01458-y","url":null,"abstract":"<p><strong>Objectives: </strong>Lacticaseibacillus rhamnosus is a widely studied probiotic species with notable functional diversity among strains. To expand the genomic resources available for this species and to support future comparative and probiotic-related studies, we sequenced and analyzed the complete genome of L. rhamnosus B34-0-2, a strain isolated from Panax ginseng, with a focus on its genomic features potentially associated with probiotic-related traits.</p><p><strong>Data description: </strong>Genomic DNA was extracted and sequenced using a combination of PacBio long-read and Illumina short-read platforms. The assembled genome comprised 2,810 predicted coding sequences (CDSs), 59 tRNA genes, and 15 rRNA genes. Functional classification assigned 2,761 CDSs (98.25%) to Clusters of Orthologous Groups (COG) categories. Screening for bacteriocin-related genes identified three genomic regions with partial similarity; however, none satisfied the predefined criteria for confident bacteriocin annotation. No antibiotic resistance genes meeting the predefined identity and coverage thresholds were detected using the CARD database. Functional annotation revealed 37 reductase-related and 3 oxidase-related genes. Phylogenetic analysis based on the 16 S rRNA gene sequence indicated that the strain clusters with L. rhamnosus strain NGRI04. These genome data provide a genomic resource for future studies on functional characterization and probiotic-related properties.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148450863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of the secretome of Microbotryum intermedium, as well as candidate fungal effectors. 微生物培养基分泌组的预测,以及候选真菌效应物。
IF 2.5
BMC genomic data Pub Date : 2026-07-13 DOI: 10.1186/s12863-026-01469-9
Roxanne K Hayes, Michael H Perlin
{"title":"Prediction of the secretome of Microbotryum intermedium, as well as candidate fungal effectors.","authors":"Roxanne K Hayes, Michael H Perlin","doi":"10.1186/s12863-026-01469-9","DOIUrl":"https://doi.org/10.1186/s12863-026-01469-9","url":null,"abstract":"<p><strong>Introduction: </strong>Secreted proteins are known to be an important virulence factor in the successful invasion and colonization of the host by fungi, especially for biotrophic parasites/pathogens of plants. To predict protein secretion, a genome must be evaluated by software that interrogates the genome for conserved sequences characteristic of known secreted proteins.</p><p><strong>Objectives: </strong>This work sought to identify putative secreted proteins of Microbotryum intermedium, a smut fungus found on plants of the Scabiosa family. To accomplish this, we used a pipeline of computational tools to serve as an efficient means of identifying potential targets as fungal effectors that can later be evaluated experimentally. So, this initial identification is ideally the first step in a larger investigation of the role of protein secretion in the development and progression of disease.</p><p><strong>Description: </strong>A pipeline of computational tools was used to stringently predict secreted proteins for Microbotryum intermedium, The pipeline was used to predict the canonical secretome of this fungus. The annotated M. intermedium genome (mycocosm.jgi.doe.gov/Micin1/Micin1.home.html) has 8,148 predicted genes, of which, only 296 were classified as putative secreted proteins using the stringent pipeline for canonical secretion prediction. These data inform future functional analyses that test candidates for their roles in pathogenicity.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148439135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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