BMC genomic dataPub Date : 2025-02-15DOI: 10.1186/s12863-025-01303-8
Yu Wan, Rachel Pike, Alessandra Harley, Zaynab Mumin, Isabelle Potterill, Danièle Meunier, Mark Ganner, Maria Getino, Juliana Coelho, Elita Jauneikaite, Kartyk Moganeradj, Colin S Brown, Alison H Holmes, Alicia Demirjian, Katie L Hopkins, Bruno Pichon
{"title":"Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.","authors":"Yu Wan, Rachel Pike, Alessandra Harley, Zaynab Mumin, Isabelle Potterill, Danièle Meunier, Mark Ganner, Maria Getino, Juliana Coelho, Elita Jauneikaite, Kartyk Moganeradj, Colin S Brown, Alison H Holmes, Alicia Demirjian, Katie L Hopkins, Bruno Pichon","doi":"10.1186/s12863-025-01303-8","DOIUrl":"10.1186/s12863-025-01303-8","url":null,"abstract":"<p><strong>Objective: </strong>Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.</p><p><strong>Data description: </strong>We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"12"},"PeriodicalIF":1.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426727","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":"Genome-wide DNA polymorphisms in two peatland adapted Coffea liberica varieties.","authors":"Tisha Melia, Fatayat, Ninik Nihayatul Wahibah, Siti Fatonah, Dewi Indriyani Roslim, Arisman Adnan","doi":"10.1186/s12863-025-01305-6","DOIUrl":"10.1186/s12863-025-01305-6","url":null,"abstract":"<p><strong>Objectives: </strong>Coffea liberica is one of the species within the Coffea genus known for its distinctive flavor and resistance to leaf rust disease. Through breeding approaches, two superior varieties of C. liberica, designated as Liberoid Meranti 1 (Lim 1) and Liberoid Meranti 2 (Lim 2), were introduced in 2015. These varieties are known for their high adaptability in peatlands. The genetic basis of plant adaptability to peatlands remains largely unknown. It is therefore essential to identify genome-wide DNA polymorphisms in Lim 1 and 2 in order to gain insights into its capacity for adaptation in peatlands.</p><p><strong>Data description: </strong>Whole genome sequencing was performed on three plants from each variety (Lim 1 and 2), resulting in 430 million sequencing reads. The mean depth of sequencing for each sample was 36.90x. The reads were mapped to the Coffea canephora genome, with an average mapping rate of 96.34%. The sequencing data revealed the presence of 3,766,805 single-nucleotide polymorphisms (SNPs) and 1,123,683 insertion-deletions (indels) in all six plants. Among the SNPs, there was a notable prevalence of transitions, with a ratio of approximately twofold compared to transversions. The generated data offers invaluable genomic resources for marker development, with significant implications for understanding peatlands adaptability.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"11"},"PeriodicalIF":1.9,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426733","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}
BMC genomic dataPub Date : 2025-01-29DOI: 10.1186/s12863-025-01301-w
Rebecca Lelievre, Mohan Rakesh, Pirro G Hysi, Julian Little, Ellen E Freeman, Marie-Hélène Roy-Gagnon
{"title":"Evaluating vitamin C-related gene-environment and metabolite-environment interaction effects on intraocular pressure in the Canadian Longitudinal Study on Aging.","authors":"Rebecca Lelievre, Mohan Rakesh, Pirro G Hysi, Julian Little, Ellen E Freeman, Marie-Hélène Roy-Gagnon","doi":"10.1186/s12863-025-01301-w","DOIUrl":"https://doi.org/10.1186/s12863-025-01301-w","url":null,"abstract":"<p><p>High intraocular pressure (IOP) is an important risk factor for glaucoma, which is influenced by genetic and environmental factors. However, the etiology of high IOP remains uncertain. Metabolites are compounds involved in metabolism which provide a link between the internal (genetic) and external environments. O-methylascorbate has been reported to be associated with IOP. In addition, researchers have identified several genetic variants which are associated with metabolite concentrations, including O-methylascorbate and another vitamin C related metabolite, ascorbic acid 2-sulfate. We aimed to understand how O-methylascorbate and ascorbic acid 2-sulfate, or genetic variants associated with these metabolites, modify the associations between dietary environmental variables and IOP. We used data from 8060 participants of the Canadian Longitudinal Study on Aging. Using linear models adjusted for relevant covariates, we tested for interactions between six genetic variants previously found to be associated with O-methylascorbate and ascorbic acid 2-sulfate and four environmental variables related to diet (alcohol consumption frequency, smoking status, fruit consumption, and vegetable consumption). We also tested for interactions between serum concentrations of O-methylascorbate and ascorbic acid 2-sulfate and these environmental factors. We used a False Discovery Rate approach to correct for the 32 interaction tests performed. One interaction was suggestively significant after multiple testing correction (adjusted P-value < 0.1): rs8050812 and alcohol consumption frequency. Understanding how genetic variants and metabolites interact with the environment could shed light on biological pathways controlling IOP and lead to improved prevention and treatment of glaucoma.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"10"},"PeriodicalIF":1.9,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070010","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}
BMC genomic dataPub Date : 2025-01-27DOI: 10.1186/s12863-025-01295-5
Yahui Gao, George E Liu, Li Ma, Cong-Jun Li, Ransom L Baldwin
{"title":"A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle.","authors":"Yahui Gao, George E Liu, Li Ma, Cong-Jun Li, Ransom L Baldwin","doi":"10.1186/s12863-025-01295-5","DOIUrl":"10.1186/s12863-025-01295-5","url":null,"abstract":"<p><strong>Objective: </strong>As one of the most important ruminant breeds, Holstein cattle supply a significant portion of milk and dairy for human consumption, playing a crucial role in agribusiness. The goal of our study was to examine the molecular adaptation of gastrointestinal tissues that facilitate milk synthesis in dairy cattle. DATA DESCRIPTION: We performed RNA-seq analysis on epithelial cells from the rumen, duodenum, and colon at eight different time points: Days 3, 14, 28, 45, 120, 220, and 305 in milk, as well as the dry period. Samples were taken from five multiparous dairy cows as biological replicates per tissue per stage, except for Days 14 and 28, for which the sample size was three. These tissues each serve critical and distinct roles in the digestion and absorption of nutrients and are all vital for providing the necessary substrates required for milk production. Understanding the intricate connections between the tissues involved in providing nutrients necessary to support milk synthesis and their role in digestion can deepen the understanding of lactation physiology. This resource aims to deliver in-depth insights into cattle lactation, highlighting the distinct traits of gastrointestinal tissues and illuminating the intricate transcriptomic dynamics throughout the lactation period.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"9"},"PeriodicalIF":1.9,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143054409","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}
BMC genomic dataPub Date : 2025-01-24DOI: 10.1186/s12863-025-01297-3
Zongping Sun, Fan Zhang, Nana Zhong, Kang Zhou, Jun Tang
{"title":"Genome sequence resources for three strains of the genus Clonostachys.","authors":"Zongping Sun, Fan Zhang, Nana Zhong, Kang Zhou, Jun Tang","doi":"10.1186/s12863-025-01297-3","DOIUrl":"10.1186/s12863-025-01297-3","url":null,"abstract":"<p><strong>Objective: </strong>Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.</p><p><strong>Data description: </strong>Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224 bp with a GC content of 48.58%, 58,114,960 bp with a GC content of 47.74% and 58,450,453 bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"8"},"PeriodicalIF":1.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043828","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}
BMC genomic dataPub Date : 2025-01-22DOI: 10.1186/s12863-025-01298-2
Shuo Jiang, Mengmin Ye, Ke Liu, Huiluo Cao, Xiaoshan Lin
{"title":"Complete genome sequence of Pseudomonas aeruginosa YK01, a sequence type 16 isolated from a patient with keratitis.","authors":"Shuo Jiang, Mengmin Ye, Ke Liu, Huiluo Cao, Xiaoshan Lin","doi":"10.1186/s12863-025-01298-2","DOIUrl":"10.1186/s12863-025-01298-2","url":null,"abstract":"<p><strong>Objectives: </strong>Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is frequently associated with multidrug resistance and global epidemic outbreaks, contributing significantly to morbidity and mortality in hospitalized patients. However, P. aeruginosa belonging to the sequence type (ST) 16 was rarely reported. Here, this report presents the complete genome sequence of YK01, a ST16 P. aeruginosa isolate from a patient with keratitis. The complete reference genome of P. aeruginosa YK01 is expected to provide valuable data for investigating its genomic population, enhancing understanding of genetic basis of P. aeruginosa species complex.</p><p><strong>Data description: </strong>A complete genome of 6.3 Mb was obtained for P. aeruginosa YK01 by combining Illumina 150-bp short reads and Nanopore long reads. The assembly is fully complete with chromosomal genome size of 6,183,266 bp, presenting a GC content of 66.7%, and a plasmid with the size of 46,067 bp, presenting GC content of 59.0%. Predicted chromosomal genomic features include 5,709 CDS, 12 rRNAs, 63 tRNAs, 4 ncRNAs, and 5,788 genes. To our knowledge, this genome data represents the first complete genome of P. aeruginosa ST16, providing crucial information for further comparative genome analysis.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"7"},"PeriodicalIF":1.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11753164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026070","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":"Assembly and characterization of the complete mitogenome of Bauhinia purpurea (Leguminosae).","authors":"Siqi Xie, Yong Chen, Danjing Zheng, Shukai Luo, Shiyuan Meng, Yan Zhong","doi":"10.1186/s12863-025-01296-4","DOIUrl":"10.1186/s12863-025-01296-4","url":null,"abstract":"<p><strong>Objective: </strong>Mitochondrial genome sequences are very useful for understanding the mitogenome evolution itself and reconstructing phylogeny of different plant lineages. Bauhinia purpurea, a species from the legume family Leguminosae, is widely distributed in South China and has high ornamental value. Here, we sequenced and assembled the mitogenome of B. purpurea to provide a useful genetic resource for further evolutionary studies.</p><p><strong>Data description: </strong>We assembled and characterized the complete mitogenome of B. purpurea based on Illumina sequence data. The mitogenome size was 525,727 bp, and its GC content was 45.38%. A total of 35 protein-coding genes, 16 tRNA genes, and 3 rRNA genes were identified in the mitogenome. We also identified 124 pairs of repeats and 6 mitogenome sequences of plastid origin (MTPTs). These MTPTs range from 108 bp to 751 bp, covering 0.65% of the mitogenome.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"6"},"PeriodicalIF":1.9,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017246","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}
BMC genomic dataPub Date : 2025-01-17DOI: 10.1186/s12863-025-01300-x
Min-Kyu Park, Yeong-Jun Park, Myung-Suk Kang, Min-Ha Kim, Soo-Young Kim, Jae-Ho Shin
{"title":"Complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770 from coal mine of Hongcheon on Republic of Korea.","authors":"Min-Kyu Park, Yeong-Jun Park, Myung-Suk Kang, Min-Ha Kim, Soo-Young Kim, Jae-Ho Shin","doi":"10.1186/s12863-025-01300-x","DOIUrl":"10.1186/s12863-025-01300-x","url":null,"abstract":"<p><strong>Objectives: </strong>The data were collected to obtain the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from the rhizosphere of Sasamorpha in a heavy metal-contaminated coal mine in Hongcheon, Republic of Korea. The objective was to explore the strain's genetic potential for plant growth promotion and heavy metal resistance, particularly arsenate and copper. The aim focused on identifying microbes that enhance plant growth in metal-tolerant environments and evaluating the strain's bioremediation and agricultural uses. This study sought key genes for bioremediation and agricultural applications in contaminated soils, aiding sustainable management and biotechnology.</p><p><strong>Data description: </strong>We report the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from a coal mine in Hongcheon, Republic of Korea. The genome contains a chromosome (4,403,796 bp) and a plasmid (74,326 bp, named pMK-1) with 286-fold coverage. Genome annotation identified 4,209 genes, including 3,926 protein-coding genes, 51 tRNA genes, and 15 rRNA genes, with a G + C content of 66.1%. Functional analysis revealed genes related to plant growth promotion and heavy metal resistance, such as arsenate (arsR, arsC) and copper (copC, copD) resistance genes. Genes involved in auxin biosynthesis suggest potential agricultural applications. The genome and plasmid are available in GenBank (CP041198.1, CP014497.1), offering insights into bioremediation and plant growth in metal-contaminated environments.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"5"},"PeriodicalIF":1.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017272","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":"Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations.","authors":"Kai-Cheng Chuang, Ping-Sung Cheng, Yu-Hung Tsai, Meng-Hsiun Tsai","doi":"10.1186/s12863-024-01293-z","DOIUrl":"10.1186/s12863-024-01293-z","url":null,"abstract":"<p><strong>Background: </strong>miRNAs (microRNAs) are endogenous RNAs with lengths of 18 to 24 nucleotides and play critical roles in gene regulation and disease progression. Although traditional wet-lab experiments provide direct evidence for miRNA-disease associations, they are often time-consuming and complicated to analyze by current bioinformatics tools. In recent years, machine learning (ML) and deep learning (DL) techniques are powerful tools to analyze large-scale biological data. Hence, developing a model to predict, identify, and rank connections in miRNAs and diseases can significantly enhance the precision and efficiency in investigating the relationships between miRNAs and diseases.</p><p><strong>Results: </strong>In this study, we utilized miRNA-disease association data obtained by biotechnological experiments to develop a DL model for miRNA-disease associations. To improve the accuracy of prediction in this model, we introduced two labeling strategies, weight-based and majority-based definitions, to classify miRNA-disease associations. After preprocessing, data was trained with a novel model combining gated recurrent units (GRU) and graph convolutional network (GCN) to predict the level of miRNA-disease associations. The miRNA-disease association datasets were from HMDD (the Human miRNA Disease Database) and categorized by two distinct labeling approaches, weight-based definitions and majority-based definitions. We classified the miRNA-disease associations into three groups, \"upregulated\", \"downregulated\" and \"nonspecific\", by regression analysis and multiclass classification. This GRU-GCN coordinated model achieved a robust area under the curve (AUC) score of 0.8 in all datasets, demonstrating the efficacy in predicting potential miRNA-disease relationships.</p><p><strong>Conclusions: </strong>By introducing innovative label-preprocessing methods, this study addressed the relationships between miRNAs and diseases, and improved the ambiguity of the results in different experiments. Based on these refined label definitions, we developed a DL-based model to refine and predict the results of associations between miRNAs and diseases. This model offers a valuable tool for complementing traditional experimental methods and enhancing our understanding of miRNA-related disease mechanisms.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"4"},"PeriodicalIF":1.9,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985591","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}
BMC genomic dataPub Date : 2025-01-13DOI: 10.1186/s12863-024-01294-y
Jiao Wang, Lei Sun, Bo Jiao, Pu Zhao, Tianyun Xu, Sa Gu, Chenmin Huo, Jianzhou Pang, Shuo Zhou
{"title":"Integrated metabolomic and transcriptomic analysis of anthocyanin metabolism in wheat pericarp.","authors":"Jiao Wang, Lei Sun, Bo Jiao, Pu Zhao, Tianyun Xu, Sa Gu, Chenmin Huo, Jianzhou Pang, Shuo Zhou","doi":"10.1186/s12863-024-01294-y","DOIUrl":"10.1186/s12863-024-01294-y","url":null,"abstract":"<p><strong>Background: </strong>Wheat seeds display different colors due to the types and contents of anthocyanins, which is closely related to anthocyanin metabolism. In this study, a transcriptomic and metabolomic analysis between white and purple color wheat pericarp aimed to explore some key genes and metabolites involved in anthocyanin metabolism.</p><p><strong>Results: </strong>Two wheat cultivars, a white seed cultivar Shiluan02-1 and purple seed cultivar Hengzi151 were used to identify the variations in differentially expressed genes (DEGs) and differentially accumulated flavonoids (DAFs). Based on metabolomic data, 314 metabolites and 191 DAFs were identified. Chalcone, flavonol, pro-anthocyanidin and anthocyanidin were the most differentially accumulated flavonoid compounds in Hengzi151. 2610 up-regulated and 2668 down-regulated DEGs were identified according to transcriptomic data. The results showed that some structural genes in anthocyanin synthesis pathway were prominently activated in Hengzi151, such as PAL, CAD, CHS and so on. Transcription factors (TFs) of MYB, bHLH, WD40 and some other TFs probably involved in regulating anthocyanin biosynthesis were identified. Some genes from hormone synthetic and signaling pathways that may participate in regulating anthocyanin biosynthesis also have been identified.</p><p><strong>Conclusions: </strong>Our results provide valuable information on the candidate genes and metabolites involved in the anthocyanin metabolism in wheat pericarp.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"3"},"PeriodicalIF":1.9,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980939","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}