BMC genomic data最新文献

{"title":"Complete genome sequence of Streptococcus sp. strain KHUD_013 isolated from the human buccal mucosa.","authors":"Doyun Ku, Seok Bin Yang, Kyu Hwan Kwack, Eun-Young Jang, Soo-Kyung Jun, Ji-Hoi Moon, Jae-Hyung Lee","doi":"10.1186/s12863-026-01438-2","DOIUrl":"10.1186/s12863-026-01438-2","url":null,"abstract":"<p><strong>Objective: </strong>The genus Streptococcus constitutes a major component of the human oral microbiome and exhibits substantial genomic diversity at the species level. However, complete and high-quality reference genomes remain limited for many closely related oral streptococci, constraining accurate comparative and taxonomic analyses. The objective of this Data Note was to generate and report a complete genome sequence of Streptococcus sp. strain KHUD_013, isolated from the human buccal mucosa, and to provide a genomic context for comparison with closely related species.</p><p><strong>Data description: </strong>Long-read sequencing using the PacBio Revio platform generated 89,500 high-fidelity (HiFi) reads with a mean read length of 6,960 bp. Genome assembly produced a single circular chromosome of 1,988,919 bp with a G + C content of 42.5%. Genome annotation identified 1,827 protein-coding genes, four ribosomal RNA operons (5 S, 16 S, and 23 S), and 62 transfer RNA genes, with an estimated completeness of 98.8%. Average Nucleotide Identity (ANI) analysis indicated that strain KHUD_013 is most closely related to the Streptococcus ilei type strain (GCA_000479335.1), with a value of 94.39% and an alignment coverage of 86.55%, consistent with genomic divergence at the species boundary. Comparative genomic analysis with four publicly available S. ilei genomes identified 179 gene clusters unique to KHUD_013, predominantly associated with replication, recombination, and repair, as well as cell wall and membrane biogenesis and transcription. This genome sequence provides a valuable resource for strain-level comparative and taxonomic studies of oral streptococci.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058589","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":"Comparative transcriptome analysis provides insights into the dwarfing mechanism of pear trees.","authors":"Yi Xiao, Qionghou Li, Shuo Li, Kaijie Qi, Yuan Gao, Hongxiang Li, Hanghang Du, Ke Ma, Shaoling Zhang, Xin Qiao","doi":"10.1186/s12863-026-01437-3","DOIUrl":"10.1186/s12863-026-01437-3","url":null,"abstract":"<p><strong>Background: </strong>Dwarfism is crucial for intensive cultivation and labor-saving management in modern orchards. However, the molecular mechanisms underlying pear tree dwarfing remain largely unclear. Here, we performed comparative transcriptome analysis between dwarf pear germplasm and pear cultivar 'Cuiguan'.</p><p><strong>Results: </strong>The dwarf pear germplasm exhibited significantly shorter internode and branch length compared to 'Cuiguan'. Histological analysis revealed that cortical cells in the dwarf pear germplasm were disordered and irregular, and longer than those of 'Cuiguan'. Comparative transcriptome analysis of shoot apex from young shoots of the dwarf germplasm and 'Cuiguan' was conducted and a total of 13,169 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that functional terms related to plant hormone biosynthesis and signal transduction were overrepresented in DEGs. Genes involved in brassinosteroid (BR) and gibberellin (GA) biosynthesis were downregulated in the dwarf germplasm. DEGs involved in transcription regulation and cell wall formation were also identified, which play potential roles in tree dwarfing. In addition, expression level of genes within the chromosomal region containing PcDw locus, which has been reported as the dominant gene controlling dwarf trait, was investigated in both the dwarf pear germplasm and 'Cuiguan'. Based on comparative analysis, nine genes in this region are considered to be closely associated with dwarf traits.</p><p><strong>Conclusions: </strong>The dwarf germplasm and 'Cuiguan' showed distinct tissue structure, with dwarfism mainly associated with defects in cell division and elongation. Comparative transcriptome analysis identified a set of DEGs involved in plant hormones biosynthesis, signaling and transport, as well as cell wall biosynthesis, modification and degradation. By integrating transcriptome data with information related to the PcDW locus, nine genes were identified as key candidates. Overall, the results of this study provide insights for understanding the mechanisms underlying pear dwarfism.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13366728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147976387","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":"Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with elevated mean corpuscular volume (MCV) and bilirubin.","authors":"Zhen Wang, Xiao-Hua Yu, Jian-Lian Liang, Zhi-Xiao Chen, Yu-Chan Huang, Yan-Qing Zeng, Li-Ye Yang","doi":"10.1186/s12863-026-01432-8","DOIUrl":"10.1186/s12863-026-01432-8","url":null,"abstract":"<p><strong>Background: </strong>Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common hereditary hemolytic disorder. To provide evidence for the clinical evaluation and management of this disorder, we investigated the differences in erythrocyte and biochemical parameters between G6PD-deficient and G6PD-normal individuals. After excluding samples with positive preliminary thalassemia screening, anemia, or liver dysfunction, a total of 2,582 health checkup individuals, 236 male military conscripts, and 3,125 males undergoing preconception check-ups were enrolled. All subjects were divided into a G6PD-normal group (G6PD-N group) and a G6PD-deficient group (G6PD-D group) using G6PD/6PGD ratio or quantitative G6PD activity assay. Statistical analyses were performed to compare erythrocyte and biochemical parameters between the two groups. Additionally, 151 samples with macrocytosis (mean corpuscular volume [MCV] > 100 fL) were subjected to G6PD/6PGD determination and genetic testing to investigate the prevalence of G6PD deficiency in this subpopulation.</p><p><strong>Results: </strong>Across all study populations, MCV and bilirubin were significantly higher in the G6PD-D group than in the G6PD-N group (p < 0.05). Except for the female health checkup group (G6PD activity), red blood cell (RBC) counts were lower in the G6PD-D group in all other populations. In addition, hemoglobin (HGB) levels were significantly lower in the G6PD-D group in the health checkup population (G6PD/6PGD method) (p < 0.05). Among the 151 \"healthy\" macrocytosis samples, 90 cases (59.60%, 90/151) were identified as G6PD-deficient, representing a significantly higher prevalence compared to the general study population.</p><p><strong>Conclusions: </strong>Reduced erythrocyte survival induced by G6PD deficiency may trigger compensatory bone marrow hyperplasia, which increases the proportion of newly synthesized erythrocyte and thereby elevates MCV. In endemic areas of G6PD deficiency, a marked increase in MCV may serve as a potential indicator for the diagnosis of G6PD deficiency.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876453","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 of Priestia megaterium MHES4, a biofertilizer candidate isolated from tomato rhizosphere in Bangladesh.","authors":"Md Nazmul Hannan, Sabbir Khan, Naim Siddique, Md Nayeem Hossain, Rifat Islam, Kamrun Nahar, G K M Mustafizur Rahman, Habibul Bari Shozib, Abul Hossain Molla, M Nazmul Hoque, Md Manjurul Haque","doi":"10.1186/s12863-026-01431-9","DOIUrl":"10.1186/s12863-026-01431-9","url":null,"abstract":"<p><strong>Objective: </strong>The genus Priestia has recently gained attention for its plant growth-promoting potential. To examine the genomic traits and biosafety profile for potential field application as a native, climate-smart bioinoculant, we sequenced, assembled and annotated the genome of Priestia megaterium strain MHES4, isolated from the rhizosphere of tomato plant grown in drought-prone ecosystem of Rajshahi, Bangladesh.</p><p><strong>Data description: </strong>Genome assembly data from the shotgun whole genome sequencing (WGS) of the P. megaterium MHES4 revealed 60 contigs with a total length of 5,267,048 bp, an N₅₀ of 446,003 bp and 37.9% G + C content. The mean sequencing depth was 127.58×, with 100% breadth of coverage. Genome completeness assessed was 97.43% with 3.5% contamination, confirming high assembly quality. In total, 5,484 protein-coding genes were annotated. Additionally, 5,445 protein-coding sequences, 28 tRNAs, and 5 rRNAs were identified. Functional analysis identified gene clusters involved in the synthesis of secondary metabolites, such as phytoene synthase and alpha-amylase, and a Type I CRISPR-Cas system. Biosafety assessment using in silico tools detected no virulence factors or transmissible antibiotic resistance genes, indicating its potential safe use in agriculture. Overall, this genomic resource provides valuable insights into the genetic potential of P. megaterium MHES4 for nutrient cycling and adaptation to the rhizosphere environment.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13330037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864855","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":"Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam.","authors":"Yu Wan, Joshua L C Wong, Julia Sanchez-Garrido, Wen Wen Low, Jane F Turton, Fabio Morecchiato, Ilaria Baccani, Kirsty Dodgson, Gian Maria Rossolini, Neil Woodford, Gad Frankel, Elita Jauneikaite, Danièle Meunier, Katie L Hopkins","doi":"10.1186/s12863-026-01421-x","DOIUrl":"10.1186/s12863-026-01421-x","url":null,"abstract":"<p><strong>Background: </strong>Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital.</p><p><strong>Methods: </strong>Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation. Mutagenesis experiments were performed to verify predicted functional alterations.</p><p><strong>Results: </strong>All isolates belonged to clone ST8134 and carried bla_KPC-2 alleles (KpMVR1: bla_KPC-157; KpMVS1 and KpMVS2: bla_KPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a frameshift mutation in KpMVR1's ompK36 gene, reducing susceptibility to meropenem-vaborbactam and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact, iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate.</p><p><strong>Conclusions: </strong>KpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance profile through within-patient evolution. This study highlights the importance of routine screening for resistant pathogens in vulnerable patients to guide antimicrobial chemotherapy and the need to characterise underlying resistance mechanisms to assess the risk of onward dissemination.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13182041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864843","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":"Single-cell genomic analysis of cancer cells from one treatment-naïve patient with metastatic prostate cancer.","authors":"Juan Jovel, Bernhard Polzer, Jordan Patterson, Hou Yong, Catalina Vasquez, Sandra O'keefe, Desmond Pink, Guibo Li, Adrian Fairey, Benjamin Adam, Jeremy Teitelbaum, Amir Salimi, Stefan Kirsh, Barbara Alberter, Lori Lowes, Eric Carpenter, Michael Kolinsky, Zhongyi Zhu, Qing Zhou, Peter Venner, Christopher Venner, David Williams, Alison Allan, Paul C Boutros, Christoph A Klein, Gane Wong, John D Lewis","doi":"10.1186/s12863-026-01435-5","DOIUrl":"10.1186/s12863-026-01435-5","url":null,"abstract":"<p><strong>Background: </strong>Prostate cancer is among the most prevalent malignancies in men and a leading cause of cancer mortality worldwide. While localized prostate cancer is often curable, progression to metastatic and castration-resistant disease either in lymph nodes or bone/bone marrow remains the major cause of death. Understanding the genomic events that drive metastasis-particularly in treatment-naïve patients-is critical to improving early detection and individualized therapy. Bulk tumor sequencing has revealed key mutational signatures but cannot resolve the cellular heterogeneity and clonal dynamics underlying metastatic spread. Single-cell genomic approaches now enable high-resolution dissection of tumor evolution, uncovering the diversity of cancer clones across disease sites.</p><p><strong>Results: </strong>We performed whole-genome and whole-exome sequencing on single cancer cells from a treatment-naïve patient with metastatic prostate cancer, isolating cells from the primary tumor, circulating tumor cells (CTCs), disseminated tumor cells (DTCs) in bone marrow, and metastatic bone lesions. Copy number aberrations (CNAs) and single-nucleotide variants (SNVs) were characterized to define genomic heterogeneity and infer clonal relationships. Frequent monoallelic losses in tumor suppressors (PTEN, TP53, FOXO4, STAG2) and gains in oncogenes (MTOR, RAF1, HRAS) and an angiogenic growth factor (VEGFB), were observed. Metastatic cells displayed fewer genomic alterations than CTCs or DTCs. While this observation is consistent with the hypothesis that metastatic competence may be associated with relative genomic stability, normal cell contamination of the metastatic biopsy cannot be excluded, and this interpretation should be considered preliminary. Clonal evolution analysis revealed a complex branching pattern consistent with multidirectional dissemination, suggesting bidirectional seeding between the primary tumor, circulation, and metastatic sites as one possible model of spread, though alternative explanations including phylogenetic reconstruction artefacts cannot be excluded from a single-patient study.</p><p><strong>Conclusions: </strong>This study provides a single-cell genomic map of metastatic prostate cancer from a treatment-naïve patient, highlighting the coexistence of diverse subclones across disease sites and supporting a multidirectional model of cancer spread.These findings raise the hypothesis that metastatic progression can emerge from multiple subclones with distinct CNA and SNV profiles. Single-cell genomic profiling of untreated tumors represents a promising approach to reconstruct clonal evolution and inform precision therapies targeting early metastatic lineages, though validation in larger patient cohorts will be required.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846791","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":"A draft genome assembly of the planorbid snail Armiger crista (Hygrophila, Planorbiidae).","authors":"Panagiota Kotsakiozi, Marina Karoumpali, Erika Šlachtová, Elena Sarropoulou, Maria Stoumpoudi, Aristeidis Parmakelis","doi":"10.1186/s12863-026-01434-6","DOIUrl":"10.1186/s12863-026-01434-6","url":null,"abstract":"<p><strong>Objectives: </strong>The draft genome assembly was generated within the framework of a greater study aiming to investigate the differences in genomic features characterizing freshwater gastropod species differing in their threat status according to the IUCN assessments.</p><p><strong>Data description: </strong>Mollusca is among the most species-rich animal groups, yet their genomes are underrepresented in genomic databases. Major drawbacks for this are the complexity of Mollusca genomes as well as the fact that due to the presence of mucopolysaccharides in their tissues, they tend to provide low quality DNA extracts. Therefore, the generation of high-quality Molluscan genome assemblies is a challenging issue. The A. crista draft genome of the present study will serve as an addition to the planorbid genomes assembled today representing three different genera (Anisus, Biomphalaria, Bulinus). Therefore, it will serve as an additional genomic asset in the effort to elucidate the ecology, evolution and taxonomy of the highly diverse taxon of Mollusca.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857831","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":"Transcriptomic analysis of Toona sinensis leaves with eight different colors at various developmental stages.","authors":"Lei Wang, Mei Yu, Dan Wu, Zhi-Gang Bao, Lu Lu, Chun-Long Zhai, Kun Liu, Yi-Zeng Lu, Yong-Jun Zhao","doi":"10.1186/s12863-026-01433-7","DOIUrl":"10.1186/s12863-026-01433-7","url":null,"abstract":"<p><p>Toona sinensis, a medicinal and edible plant, holds economic and ecological significance in Asia. Despite its diverse applications, the genetic basis of leaf color formation remains unclear. This study aimed to investigate the molecular mechanisms underlying color variations across three cultivars (red, brown, green) at different developmental stages. Young tender leaflets from apical tips and fully expanded leaflets from basal positions of the same compound leaf were collected for RNA-Seq analysis. Differential expression analysis revealed significant enrichment of genes involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, and carotenoid metabolism pathways, suggesting their key roles in pigment accumulation. These metabolites are not only critical for coloration but also contribute to disease resistance and antioxidation. This research provides novel insights into the genetic regulatory networks governing leaf color formation in T. sinensis, facilitating molecular breeding for color trait improvement.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857801","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":"TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.","authors":"Alsayed Alfiky, Said A Dora","doi":"10.1186/s12863-026-01429-3","DOIUrl":"10.1186/s12863-026-01429-3","url":null,"abstract":"<p><p>The ecological versatility of the fungal genus Trichoderma spans roles from mycoparasite to saprotroph, presenting a compelling model to investigate how genomic variation underpins niche adaptation. However, comparative genomic studies of Trichoderma are hampered by inconsistent annotation methods across independently sequenced genomes, complicating direct cross-species analysis. To address this, we developed and applied a unified, evidence-based annotation pipeline integrating RNA-seq and homology data to six key species spanning the genus's ecological range (T. asperellum, T. harzianum, T. virens, T. reesei, T. longibrachiatum, and T. citrinoviride). This work presents 'TrichoBase', a consistently annotated genomic resource comprising standardized gene models, functional annotations, and comparative profiles. Using this comparable dataset, we confirm and quantitatively refine the correlation between transposable element (TE) accumulation and genome size expansion. We further demonstrate that TE-rich genomes of mycoparasitic strains are enriched in carbohydrate-active enzymes (CAZymes) and biosynthetic gene clusters (BGCs), while saprotrophic opportunistic lineages show streamlined profiles. Notably, the resource reveals patchy phylogenetic distributions of specific BGC families, such as sorbicillinoid and brefeldin A-like clusters. We provide the complete resource including annotation files, analysis scripts, and a reproducible pipeline to serve as a foundational dataset for future functional genomics and ecological studies in Trichoderma.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13196189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846839","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":"Chromosome-scale, single haploid assembly of achiote (Bixa orellana).","authors":"Meric C Lieberman, Margarita Aguilar-Espinosa, David Chan-Rodriguez, Luca Coma, Renata Rivera-Madrid, Isabelle M Henry","doi":"10.1186/s12863-026-01430-w","DOIUrl":"10.1186/s12863-026-01430-w","url":null,"abstract":"<p><strong>Objectives: </strong>Bixa orellana, commonly known as achiote, is the domesticated species within the Bixa genus. It is a commercially important plant due to its high bixin content, primarily used as a pigment in the food industry. Achiote is a cross-pollinated, highly heterozygous species with a small genome size. This study aims to generate a de novo genome assembly of Bixa orellana L., which will be crucial for identifying the genes involved in bixin synthesis and its regulation. This assembly will offer valuable insights for future applications related to agronomical traits aimed at increasing bixin yield in achiote or different plant or microorganism systems, as well as for improving the genetic potential of achiote crops.</p><p><strong>Data description: </strong>A de novo assembly of the genome of Bixa orellana L., accession PN4 was generated from ~145 x consensus coverage of PacBio long reads. This Hifiasm assembly included 10 chromosome-scale superscaffolds representing 96.4% of the assembly, for an overall genome size of 270 Mb. Illumina RNA-Seq libraries from different tissues sampled from the same cultivar were used to annotate the genome.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13154580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846793","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}