BMC Genomics最新文献

{"title":"Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment.","authors":"Hao Yang, Yu Gan, Shenghai Jiang, Xianchang Zhu, Yang Xia, Dengmei Gong, Xianrang Xie, Yao Gong, Yi Zhang, Qian Lei, Maijian Wang, Jida Li","doi":"10.1186/s12864-025-11421-3","DOIUrl":"10.1186/s12864-025-11421-3","url":null,"abstract":"<p><strong>Background: </strong>The occurrence and development of colorectal cancer (CRC) is an incredibly long process that involves continuous changes in the tumor microenvironment. These constant changes may ultimately result in genetic alterations and changes in the metabolic processes of some symbiotic bacteria as a way to adapt to the changing environment. Patients with CRC exhibit an altered abundance of Bacteroides fragilis (B. fragilis) as indicated by several studies. To better understand the genomic characteristics and virulence spectrum of B. fragilis strains in tumor tissues, B. fragilis strains were isolated from tumor and paracancerous tissues of CRC patients.</p><p><strong>Methods: </strong>The isolates were identified using 16 S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.</p><p><strong>Results: </strong>A strain of B. fragilis enterotoxin (BFT) bft1-producing ZY0302 and a non-enterotoxin-producing B. fragilis ZY0804 were isolated from cancerous and paraneoplastic tissues, respectively. Analysis based on the core and nonessential genes showed that the genomic profiles of the isolates, ZY0302 and ZY0804, differed from those of B. fragilis from other tissue sources. This core and the co-evolution of non-essential genes may be the result of their adaptation to fluctuations in the tumor microenvironment and enhancing their survival. In addition, the ZY0302 and ZY0804 genomes underwent extensive horizontal gene transfer and varying degrees of genomic rearrangements, inversions, insertions, and deletion events, which may favor the enhancement of bacteria's ability to adapt to environmental changes. For instance, the virulence factors, such as the capsular biosynthesis gene clusters and components of the type IV secretion system, acquired through horizontal gene transfer, may facilitated B. fragilis in evading immune responses and managing oxidative stress. Moreover, our analysis revealed that multiple virulence factors identified in the isolates were mainly involved in bacterial adhesion and colonization, oxidative stress, iron acquisition, and immune evasion. This observation is worth noting given that enzymes such as neuraminidase, lipase, hemolysin, protease, and phosphatase, along with genes responsible for LPS biosynthesis, which are recognized for their association with the virulence of B. fragilis, were prevalent among the isolates.</p><p><strong>Conclusions: </strong>In summary, it is our assertion that the alterations observed in both core and nonessential genes of B. fragilis, which have been isolated from tissues of colorectal cancer patients, along with significant instances of horizontal gene transfer to the genome, are likely intended to enhance adaptation to the evolving conditions of the tumor microenvironment. This study may provide new insights into the interaction between B. fragilis and the CRC","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"269"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large indel detection in region-based phased diploid assemblies from linked-reads.","authors":"Can Luo, Brock A Peters, Xin Maizie Zhou","doi":"10.1186/s12864-025-11398-z","DOIUrl":"10.1186/s12864-025-11398-z","url":null,"abstract":"<p><strong>Background: </strong>Linked-reads improve de novo assembly, haplotype phasing, structural variant (SV) detection, and other applications through highly-multiplexed genome partitioning and barcoding. Whole genome assembly and assembly-based variant detection based on linked-reads often require intensive computation costs and are not suitable for large population studies. Here we propose an efficient pipeline, RegionIndel, a region-based diploid assembly approach to characterize large indel SVs. This pipeline only focuses on target regions (50kb by default) to extract barcoded reads as input and then integrates a haplotyping algorithm and local assembly to generate phased diploid contiguous sequences (contigs). Finally, it detects variants in the contigs through a pairwise contig-to-reference comparison.</p><p><strong>Results: </strong>We applied RegionIndel on two linked-reads libraries of sample HG002, one using 10x and the other stLFR. HG002 is a well-studied sample and the Genome in a Bottle (GiaB) community provides a gold standard SV set for it. RegionIndel outperformed several assembly and alignment-based SV callers in our benchmark experiments. After assembling all indel SVs, RegionIndel achieved an overall F1 score of 74.8% in deletions and 61.8% in insertions for 10x linked-reads, and 64.3% in deletions and 36.7% in insertions for stLFR linked-reads, respectively. Furthermore, it achieved an overall genotyping accuracy of 83.6% and 80.8% for 10x and stLFR linked-reads, respectively.</p><p><strong>Conclusions: </strong>RegionIndel can achieve diploid assembly and detect indel SVs in each target region. The phased diploid contigs can further allow us to investigate indel SVs with nearby linked single nucleotide polymorphism (SNPs) and small indels in the same haplotype.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 Suppl 2","pages":"263"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional insights on the incomplete cytoplasmic maturation and developmental potential of oocytes cultured without granulosa cells in mice.","authors":"Yibo Wang, Yichuan Zhang, Tianjie Li, Yun Ren, Ping Zhou, Lin Fu, Chenxi Xiao, Ziying Huang, Hanji Huang, Wenfeng Xie, Yuxin Luo, Yanan Qi, Hongcui Zhao, Yang Yu, Yong Fan, Heng Pan","doi":"10.1186/s12864-025-11455-7","DOIUrl":"10.1186/s12864-025-11455-7","url":null,"abstract":"<p><strong>Background: </strong>Oocyte maturation is crucial for female fertility and embryonic development, encompassing nuclear and cytoplasmic maturation. Supportive cells of follicles, such as granulosa cells, are essential for oocyte growth and maturation. Oocytes can achieve nuclear maturation without granulosa cells during in vitro maturation (IVM). However, there is still a higher chance of incomplete cytoplasmic maturation for these oocytes with mature nuclei compared with oocytes cultured with granulosa cells. Oocytes with incomplete cytoplasmic maturation have lower fertilization rates and developmental potential than mature ones, although underlying mechanisms are poorly understood. Identifying key genes and signaling pathways associated with oocyte cytoplasmic maturation can help further elucidate the maturing process of oocytes and understand the impact of immature oocytes on embryonic development, throwing insights into the strategy to improve the success rate of assisted reproductive technologies.</p><p><strong>Results: </strong>Our study investigated murine oocytes maturing with and without granulosa cells. IVM without granulosa cells yielded oocytes with lower nuclear maturation rates than IVM with granulosa cells and in vivo maturation (IVO). Even though oocytes could achieve nuclear maturation without granulosa cells, they showed incomplete cytoplasmic maturation featuring higher levels of reactive oxygen species, lower mitochondrial density, and higher proportions of cells with abnormal distributions of cortical granules. Of note, oocytes with immature and mature cytoplasm had distinct transcriptional profiles. In the immature oocytes, we observed a deficient mRNA restoration of genes in crucial regulatory pathways of cellular growth and division, potentially affecting embryonic development. Differentially expressed genes (DEGs) between immature and mature oocytes were identified to be highly expressed in different pre-implantation stages, such as the MII oocyte, the 8-cell stage, and the ICM stage. Identified DEGs were enriched in key regulatory pathways of fertilization and embryonic development, such as energy and metabolic pathways. These observations indicated that the impeded development potential of oocytes with immature cytoplasm might be the result of abnormal gene expressions during oocyte maturation.</p><p><strong>Conclusions: </strong>We show that granulosa cells are important for both nuclear and cytoplasmic maturation of oocytes. Abnormal gene expression in oocytes with incomplete cytoplasmic maturation may be associated with potential defects in fertilization and embryonic development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"270"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis and functional validation of the cotton FAH gene family for salt stress.","authors":"Haijing Gu, Wenxiang Feng, Teame Gereziher Mehari, Yifan Wang, Ziyin Wang, Yifan Xu, Yizhou Zhao, Junfeng Tang, Ke Zhang, Zitong Zhou, Wei Wang, Ruqin Zhou, Jianyong Wu, Baohua Wang","doi":"10.1186/s12864-025-11450-y","DOIUrl":"10.1186/s12864-025-11450-y","url":null,"abstract":"<p><strong>Background: </strong>Fatty acid hydroxylases (FAHs) are a family of enzymes that includes fatty acid hydroxylases, carotenoid hydroxylases, and sterol desaturases. Fatty acids are highly important for plants. They are the main source of energy storage and the main component of the cell membrane. Saturated fatty acids can be divided into two categories: saturated fatty acids and unsaturated fatty acids. FAHs play a pivotal role in enhancing plant salt tolerance by modulating fatty acid metabolic pathways, thereby improving cell membrane stability and antioxidant capacity.</p><p><strong>Results: </strong>In this study, we identified a total of 129 FAH gene family members in four cotton species, namely, Gossypium hirsutum, Gossypium darwinii, Gossypium arboreum, and Gossypium raimondii. The FAH genes were divided into five subgroups via evolutionary analysis. FAH genes located in the same subgroup presented similar gene structures and a consistent distribution of conserved motifs through the analysis of evolutionary trees, gene structures, and conserved motifs. Chromosomal localization analysis of the FAH gene family revealed that it has undergone chromosomal segment duplication events. Analysis of cis-acting elements suggested that the FAH gene may be involved in regulating biotic and abiotic stresses, plant growth and development, signaling pathways, and other physiological processes. The RT‒qPCR results revealed significant differences in the expression levels of FAH gene family members under salt stress conditions compared with those in the control group. Additionally, we successfully silenced Gohir.A03G045300 through VIGS experiments, and the results indicated that the silenced plants were more sensitive to salt stress than the control plants were. This suggests that Gohir.A03G045300 may be involved in the response of cotton to salt stress.</p><p><strong>Conclusions: </strong>A total of 129 FAH genes were identified in four Gossypium species through bioinformatics analysis. Gene silencing of FAH members in G. hirsutum revealed that the FAH gene family plays a crucial role in the response of cotton to salt stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"271"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omic latent variable data integration reveals multicellular structure pathways associated with resistance to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion in Uganda.","authors":"Madison S Cox, Kimberly A Dill-McFarland, Jason D Simmons, Penelope Benchek, Harriet Mayanja-Kizza, W Henry Boom, Catherine M Stein, Thomas R Hawn","doi":"10.1186/s12864-025-11407-1","DOIUrl":"10.1186/s12864-025-11407-1","url":null,"abstract":"<p><p>Understanding the mechanisms of early clearance of Mycobacterium tuberculosis (Mtb) may illuminate new therapeutic strategies for tuberculosis (TB). We previously found genetic, epigenetic, and transcriptomic signatures associated with resistance (resister, RSTR) to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion among highly exposed TB contacts. We hypothesized that integration of these datasets with multi-omic latent factor methods would detect pathways differentiating RSTR patients from those with asymptomatic TB infection (TBI, also known as latent TB infection or LTBI) that were not detected in individual dataset analyses. We pre-filtered and scaled features with the largest change between TBI and RSTR groups for 126 patients with data in at least two of five data modalities: single nucleotide polymorphisms (SNP), monocyte RNAseq (baseline and Mtb-stimulated conditions), and monocyte epigenetics (methylation and ATAC-seq). Using multiomic latent factor analysis (MOFA), we generated ten latent factors on the subset of 33 patients with all five datasets available, four of which differed by RSTR status (FDR < 0.1). Factor 4 showed the greatest difference between RSTR and TBI groups (FDR < 0.001). Three additional latent factor integration methods also distinguished the RSTR and TBI groups and identified overlapping features with MOFA. Using pathway analysis and a cluster-based enrichment method, we identified functions associated with latent factors and found that MOFA Factors 2-4 include functions related to cell-cell adhesion, cell shape, and multicellular structure development. In summary, latent variable integration methods uncovered signatures associated with resistance to TST/IGRA conversion that were not detected by individual dataset analyses and included pathways associated with cellular interactions and multicellular structures.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"265"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced dynamicity: evolutionary insights into amphibian mitogenomes architecture.","authors":"Yi Xiao, Gengyun Niu, Haihe Shi, Zhenyu Wang, Renzeng Du, Yankuo Li, Meicai Wei","doi":"10.1186/s12864-025-11480-6","DOIUrl":"10.1186/s12864-025-11480-6","url":null,"abstract":"<p><p>Mitogenomes are known for their structural dynamics and the complexity of their rearrangement patterns. However, their utility in metazoan comparative biology has not been fully exploited. Vertebrate mitogenomes are now sufficiently representative to allow the development of more advanced methods for comparing genome architecture. Furthermore, the relatively robust phylogeny of vertebrates at higher taxonomic ranks allows us to infer the patterns of genome evolution accordingly. In this study, using amphibians as an example, we performed data cleaning and manual annotation on 1777 samples from the NCBI and identified 88 rearrangement types, most of which were clade-specific. In addition, we quantified genomic changes in an evolutionary framework and obtained stepwise growth curves of the architectural changes. This study provides new perspectives for understanding the evolution of the mitogenomes in amphibians and is expected to facilitate the qualitative and quantitative development of mitogenomes research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"261"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.","authors":"Hiruni A Thanthirige, Nilni A Wimalarathna, Anushka M Wickramasuriya","doi":"10.1186/s12864-025-11414-2","DOIUrl":"10.1186/s12864-025-11414-2","url":null,"abstract":"<p><strong>Background: </strong>Single nucleotide polymorphisms (SNPs) have emerged as the marker of choice in breeding and genetics, particularly in non-model organisms such as black pepper (Piper nigrum L.), a globally recognized spice crop. This study presents a comprehensive catalog of SNPs in the black pepper genome using data from 30 samples obtained from RNA sequencing and restriction site-associated DNA sequencing, retrieved from the Sequence Read Archive, and their consequences at the sequence level.</p><p><strong>Results: </strong>Three SNP calling and filtering pipelines, namely BCFtools, Genome Analysis Toolkit (GATK)-soft filtering, and GATK-hard filtering, were employed. Results revealed 498,128, 396,003, and 312,153 SNPs respectively identified by these pipelines, with 260,026 SNPs commonly detected across all methods. Analysis of SNP distribution across the 45 scaffolds of the black pepper genome showed varying densities, with pseudo-chromosomes Pn25 (0.86 SNPs/kb), Pn8 (0.74 SNPs/kb), and Pn7 (0.72 SNPs/kb) exhibiting the highest densities. Conversely, scaffolds Pn27 to Pn43 exhibited minimal SNP distribution, except Pn45. Approximately 34.80% of SNPs exhibited stronger genetic linkage (r² > 0.7). Moreover, SNPs predominately mapped to downstream (≈ 32.54%), upstream (≈ 22.52%), and exonic (≈ 16.20%) regions of genes. Transition substitution accounted for the majority (≈ 57.42%) of identified SNPs, resulting in an average transition-to-transversion ratio of 1.36. Notably, 56.09% of SNPs were non-synonymous, with a significant proportion (≈ 53.59%) being missense mutations. Additionally, 12,491 SNPs with high or moderate impacts were identified, particularly in genes associated with secondary metabolism and alkaloid biosynthesis pathways. Furthermore, the expression of 675 genes was potentially influenced by local (cis-acting) SNPs, while 554 genes were affected by distal (trans-acting) SNPs.</p><p><strong>Conclusion: </strong>The findings of the present study underscore the utility of identified SNPs and their targets, especially those impacting important pathways, for future genetic investigations and crop improvement efforts in black pepper. The characterization of SNPs in genes related to secondary metabolism and alkaloid biosynthesis highlights their potential for targeted breeding aimed at enhancing the yield, quality, and resilience of this economically important crop in diverse environmental conditions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"256"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.","authors":"Linnea K Andersen, Neil F Thompson, Jason W Abernathy, Ridwan O Ahmed, Ali Ali, Rafet Al-Tobasei, Benjamin H Beck, Bernarda Calla, Thomas A Delomas, Rex A Dunham, Christine G Elsik, S Adam Fuller, Julio C García, Mackenzie R Gavery, Christopher M Hollenbeck, Kevin M Johnson, Emily Kunselman, Erin L Legacki, Sixin Liu, Zhanjiang Liu, Brittany Martin, Joseph L Matt, Samuel A May, Caitlin E Older, Ken Overturf, Yniv Palti, Eric J Peatman, Brian C Peterson, Michael P Phelps, Louis V Plough, Mark P Polinski, Dina A Proestou, Catherine M Purcell, Sylvie M A Quiniou, Guglielmo Raymo, Caird E Rexroad, Kenneth L Riley, Steven B Roberts, Luke A Roy, Mohamed Salem, Kelly Simpson, Geofrey C Waldbieser, Hanping Wang, Charles D Waters, Benjamin J Reading","doi":"10.1186/s12864-025-11447-7","DOIUrl":"10.1186/s12864-025-11447-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"260"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SLAF-seq technology-based genome-wide association and population structure analyses of hot pepper and sweet pepper.","authors":"Yaning Meng, Hongxiao Zhang, Zhe Zhang, Xinxin Li, Zhanghong Yu, Yanqin Fan, Libin Yan","doi":"10.1186/s12864-025-11454-8","DOIUrl":"10.1186/s12864-025-11454-8","url":null,"abstract":"<p><strong>Background: </strong>Utilizing Single Nucleotide Polymorphism (SNP) marker technology, a phylogenetic and agronomic trait network analysis was conducted on the collected hot pepper and sweet pepper germplasm resources, providing a theoretical basis for parental selection and new varieties.</p><p><strong>Results: </strong>Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed for a genome-wide association study (GWAS) on 197 hot pepper and sweet pepper germplasm resources, generating 1404.88 Mb clean reads data with an average Q30 of 91.5% and mean GC content of 37.96%. Through sequencing data analysis, a total of 639,815 SLAF tags were obtained with an average sequencing depth of 12.16x, among which 86,381 were polymorphic SLAF tags, leading to the development of 18,145,155 SNP markers. The identified SNP markers were used for cluster analysis of the genetic structure and phylogenetic relationships of hot pepper and sweet pepper germplasm resources, dividing the 197 hot pepper and sweet pepper germplasm resources into 9 clusters. Additionally, a genome-wide association analysis was conducted on 25 agronomic traits of the 197 hot pepper and sweet pepper materials, yielding a substantial number of significantly associated SNP loci with agronomic traits. A correlation network analysis diagram was drawn among the various agronomic traits, preliminarily determining the relationships between the 25 agronomic characteristics of hot pepper and sweet pepper and the positions of 15 agronomic traits (p < 1.707 × 10^-8) on the chromosomes were annotated, forming multi-trait aggregation regions.</p><p><strong>Conclusions: </strong>Our research reveals the genetic diversity, phylogenetic relationships, and population structure of 197 hot pepper and sweet pepper germplasm resources, providing a basis for germplasm identification, resource utilization, and breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"258"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level genome assembly of Eimeria tenella at the single-oocyst level.","authors":"Kaihui Zhang, Yudong Cai, Yuancai Chen, Yin Fu, Ziqi Zhu, Jianying Huang, Huikai Qin, Qimeng Yang, Xinmei Li, Yayun Wu, Xun Suo, Yu Jiang, Longxian Zhang","doi":"10.1186/s12864-025-11423-1","DOIUrl":"10.1186/s12864-025-11423-1","url":null,"abstract":"<p><strong>Background: </strong>Eimeria are obligate protozoan parasites, and more than 1,500 species have been reported. However, Eimeria genomes lag behind many other eukaryotes since obtaining many oocysts is difficult due to a lack of sustainable in vitro culture, highly repetitive sequences, and mixed species infections. To address this challenge, we used whole-genome amplification of a single oocyst followed by long-read sequencing and obtained a chromosome-level genome of Eimeria tenella.</p><p><strong>Results: </strong>The assembled genome was 52.13 Mb long, encompassing 15 chromosomes and 46.94% repeat sequences. In total, 7,296 protein-coding genes were predicted, exhibiting high completeness, with 92.00% single-copy BUSCO genes. To the best of our knowledge, this is the first chromosome-level assembly of E. tenella using a combination of single-oocyst whole-genome amplification and long-read sequencing. Comparative genomic and transcriptome analyses confirmed evolutionary relationship and supported estimates of divergence time of apicomplexan parasites and identified AP2 and Myb gene families that may play indispensable roles in regulating the growth and development of E. tenella.</p><p><strong>Conclusion: </strong>This high-quality genome assembly and the established sequencing strategy provide valuable community resources for comparative genomic and evolutionary analyses of the Eimeria clade. Additionally, our study also provides a valuable resource for exploring the roles of AP2 and Myb transcription factor genes in regulating the development of Eimeria parasites.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"257"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}