BMC Genomics最新文献

{"title":"Chromosome-level genome of Cyprinus rubrofuscus ♀ × Sinocyclocheilus grahami ♂ provides high-quality parental haplotype genomes and insights into hybrid economic traits enhancement.","authors":"Yanhui Yin, Yuanwei Zhang, Anli Wu, Wei Dao, Jing Long, Xiaofu Pan, Junxing Yang, Xiaoai Wang","doi":"10.1186/s12864-025-11929-8","DOIUrl":"10.1186/s12864-025-11929-8","url":null,"abstract":"<p><p>Cyprinids, the largest and most economically significant family of teleosts, comprise over 600 polyploid species, whose genomic complexity presents challenges in deciphering the genetic basis of phenotypic diversity. In this study, we generated high-quality haplotype-resolved genomes for two representative Cyprinidae allopolyploids (Cyprinus rubrofuscus and Sinocyclocheilus grahami) by constructing the diploid genome of their hybrid (C. rubrofuscus ♀ × S. grahami ♂, CRSG). The haplotype assembly for C. rubrofuscus contained 50 chromosomes (1.5 Gb, scaffold N50 = 29.64 Mb), while S. grahami contained 48 chromosomes (1.8 Gb, scaffold N50 = 36.04 Mb). Genomic analyses refined the ancestral divergence times and provided new insights into chromosomal fusion events, gene family expansions and contractions, and positively selected genes driving phenotypic divergence between the two species. Comparative analysis of economic traits and gene expression in C. rubrofuscus, S. grahami, and their reciprocal hybrids identified several key genes associated with enhanced growth (e.g., OXPHOS-related genes), optimized fatty acid composition (e.g., tecr, acot1, acsl1, cpt2), and hybrid sterility (e.g., cyp19a1, wt1, dmrtb1). Notably, parental haplotype dominance of those genes were observed, haplotype genes derived from C. rubrofuscus (CR-Hg) predominantly contributed to the accelerated growth of reciprocal hybrids, exhibiting significantly higher expression levels of OXPHOS-related genes compared to those derived from S. grahami (SG-Hg). Conversely, SG-Hg played a central role in optimizing fatty acid composition in CRSG, with genes involved in polyunsaturated fatty acid biosynthesis and degradation showing markedly higher expression levels than their CR-Hg counterparts. Parental haplotype genes both regulated the sterility of CRSG, as no significant differences were observed between CR-Hg and SG-Hg in the sex differentiation and meiotic disorder-related genes. This study highlight the potential of C. rubrofuscus and S. grahami as genetic resources for developing hybrids with improved growth rates and optimized fatty acid profiles, provide valuable genomic resources and theoretical insights for aquaculture breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"739"},"PeriodicalIF":3.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820507","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":"First whole-genome sequence of Mycobacterium avium subsp. silvaticum isolated from a diseased Egyptian goose (Alopochen aegyptiaca).","authors":"Stefanie A Barth, Martin Peters, Sascha Mormann, Petra Möbius, Sten Calvelage, Hanka Brangsch","doi":"10.1186/s12864-025-11893-3","DOIUrl":"10.1186/s12864-025-11893-3","url":null,"abstract":"<p><strong>Background: </strong>Among the non-tuberculous mycobacteria, Mycobacterium (M.) avium are important pathogens for humans and/or animals. Currently, there are four M. avium subspecies: subsp. hominissuis (Mah), subsp. paratuberculosis (Map), subsp. avium (Maa), and subsp. silvaticum (Mas). While sufficient data is available for the first three mentioned, only few reports exist on the isolation, epidemiology and even less on the genetic equipment of Mas.</p><p><strong>Results: </strong>Here, Mas was isolated from an Egyptian goose that died of avian tuberculosis. Subspecies identification was based on the presence of IS901 and IS1245 as well as Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat analysis demonstrating Mas specific profile INMV99 profile. During cultural isolation, Mas showed preference for media with mycobactin supplementation but was not limited to mycobactin-containing media. A closed genome sequence was assembled using short- and long-read sequencing technology. The genome sequence consisted of one circular chromosome of 4.84 Mb (GC content 69.3%) and no plasmid. It was highly similar to the only other available Mas sequence (ANI 99.98%, GGDC 99.7%) and eight Maa sequences (ANI ≥99.88%, GGDC ≥98.9%), although all Maa genomes were larger (approx. 5 Mb). In silico prediction of the metabolic pathways and gene content found that all Maa but no Mas should be able to synthetize ergothioneine and the carotenoid neurosporene. The analysis of the mycobactin cluster mbt-1 made it obvious that in Mas two of the eleven mbt genes (mbtB and mbtE) were probably dysfunctional due frameshift-based disruptions.</p><p><strong>Conclusions: </strong>The first complete, high quality, closed genome sequence of a Mas isolate closes a knowledge gap. Even if the collection of further genome sequences is considered necessary, the now existing data set already enables a deeper analysis of M. avium. The found differences in the Mas gene content compared to the closest relative Maa seem to be stable and independent of spatial (France, UK, Germany) and temporal (>40 years) differences on their isolation. These data thus call into question the demand for merging the two subspecies Maa and Mas into one, but further genome sequences from other Mas strains are needed to answer this question conclusively.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"741"},"PeriodicalIF":3.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820509","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":"MEGDTA: multi-modal drug-target affinity prediction based on protein three-dimensional structure and ensemble graph neural network.","authors":"Zhanwei Hou, Yijun Li, Haixia Zhai, Junwei Luo, Yulian Ding, Yi Pan","doi":"10.1186/s12864-025-11943-w","DOIUrl":"10.1186/s12864-025-11943-w","url":null,"abstract":"<p><strong>Background: </strong>Drug development is a time-consuming and costly endeavor, and utilizing computer-aided methods to predict drug-target affinity (DTA) can significantly accelerate this process. The key to accurate DTA prediction lies in selecting appropriate computational models to effectively extract features from drug molecular structures and target protein structures. Existing methods usually ignore the features of the protein three-dimensional structure.</p><p><strong>Results: </strong>This paper proposes a multi-modal drug-target affinity prediction model based on protein three-dimensional structure and ensemble graph neural networks (MEGDTA). This model aims to capture diverse features from drug and target structure using neural network architectures, especially for protein three-dimensional structure. First, one drug is represented into two forms by a molecular graph and a Morgan Fingerprint, and their features are extracted by constructing a graph feature space and a fully connected network, respectively. Second, for a protein, a residue graph is constructed based on its three-dimensional structure. And, the protein sequence and residue graph are processed using a long short-term memory (LSTM) network and multiple parallel graph neural networks (GNNs) with variant modules to learn the latent features of proteins. Third, a cross-attention mechanism fuses the extracted features of the drug and protein, followed by fully connected layers to finalize the prediction. The source code of MEGDTA is available from https://github.com/liyijuncode/MEGDTA .</p><p><strong>Conclusions: </strong>MEGDTA is validated on three publicly available benchmark datasets, Davis, KIBA and Metz. A comparative study is conducted with other existing models. The results show that MEGDTA performs strongly in terms of mean squared error (MSE) and concordance index (CI), and r²_m, which demonstrate the effectiveness of MEGDTA.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"738"},"PeriodicalIF":3.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820510","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":"Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds.","authors":"Pengwei Ren, Yongdong Peng, Liu Yang, Muhammad Zahoor Khan, Yadi Jing, Chao Qi, Zhansheng Liu, Shuer Zhang, Nenzhu Zheng, Meixia Zhang, Xiang Liu, Zhiming Zhu, Mingxia Zhu","doi":"10.1186/s12864-025-11782-9","DOIUrl":"10.1186/s12864-025-11782-9","url":null,"abstract":"<p><strong>Background: </strong>Shandong's local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China's waterfowl germplasm. Understanding the genetic characteristics of these populations, along with monitoring and conserving their genetic diversity, is of paramount importance. In this study, we analyzed the genetic diversity, population structure, and genetic characteristic of 89 ducks, including the Weishan Partridge (WS, n = 30), Matahu (MT, n = 29), and Wendeng Black (WD, n = 30), using genome resequencing data. We also used a random forest model algorithm to identify specific breed-identification SNPs, ensuring accurate differentiation of the three breeds.</p><p><strong>Results: </strong>The findings of this study revealed that WS ducks exhibited higher genetic diversity compared to the other two breeds. This may be related to their larger group size and level of inbreeding. Notice that H_O values larger than H_E values for all three species are associated with random mating patterns, reduced selection pressure, or recovery from historical bottleneck events. Additionally, the WS and MT breeds were found to be closely related, possibly sharing a common ancestral group, while both breeds were genetically distinct from the WD breed. After comparing with meat duck breeds (BJ, CV, ML), we identified several potential functional genes (notably TP63, BMP3, and ACACA) associated with key economic traits, including growth and development, muscle quality, reproductive performance, and disease resistance. Using top 60 feature selected SNPs, the random forest classification model successfully identified different breeds of ducks under the study with 96.2% accuracy.</p><p><strong>Conclusions: </strong>This study, utilizing genome sequencing data and machine learning algorithms, provides a comprehensive evaluation of the genetic resources of Shandong's local duck breeds. It highlights the distinct genetic characteristics of the three breeds, providing valuable insights and a theoretical foundation for the conservation and sustainable utilization of Shandong's local duck genetic resources.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"734"},"PeriodicalIF":3.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12333207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803385","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":"Genomic adaptations of Vibrio campbellii to thermal and salinity stress: insights into marine pathogen resilience in a changing ocean.","authors":"Jiranan Pattano, Thitaporn Dechathai, Netnapa Chaichanit, Komwit Surachat, Korakot Wichitsa-Nguan Jetwanna, Kanchana Srinitiwarawong, Pimonsri Mittraparp-Arthorn","doi":"10.1186/s12864-025-11908-z","DOIUrl":"10.1186/s12864-025-11908-z","url":null,"abstract":"<p><strong>Background: </strong>Rising ocean temperatures and salinity fluctuations driven by climate change are reshaping marine microbial communities, including pathogenic Vibrio species. Vibrio campbellii, a major marine pathogen in shrimp aquaculture, needs to adapt to these environmental changes to survive and maintain virulence. However, the molecular mechanisms underlying its response to combined thermal and osmotic stress are largely unexplored.</p><p><strong>Results: </strong>This study examines the physiological responses of pathogenic V. campbellii strain HY01 and non-pathogenic strain ATCC BAA-1116 under combined temperature (25 °C, 30 °C, and 35 °C) and salinity (20, 30, and 60 ppt) conditions. Strain HY01 exhibited remarkable adaptability across all tested conditions, whereas ATCC BAA-1116 demonstrated reduced resilience under specific temperature-salinity combinations. Growth at 30-35 °C with elevated salinity promoted bioluminescence, swimming motility, and biofilm formation in both strains. Using transcriptomic analysis, our findings reveal that increased salinity enhances bacterial resilience under thermal stress by upregulating genes associated with metabolic pathways, oxidative phosphorylation, and ribosomal function. While elevated temperature and salinity suppress certain virulence traits (e.g., T6SS, flagellar assembly), they concurrently promote biofilm formation, enabling persistence in marine environments. Additionally, genes involved in osmoadaptation, such as those encoding compatible solutes, were highly expressed under extreme salinity. The observed shifts in gene expression highlight a coordinated regulatory network that balances cellular energy production, stress defense mechanisms, and colonization potential.</p><p><strong>Conclusions: </strong>This study provides a better understanding into the adaptive strategies of V. campbellii in response to thermal and osmotic stressors. These findings are particularly relevant for understanding how climate change-driven environmental shifts influence the ecology and pathogenicity of marine vibrios. Future studies should explore the functional consequences of these adaptations in shrimp-pathogen interactions, contributing to sustainable aquaculture practices.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"736"},"PeriodicalIF":3.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803384","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":"Identification of the putative regulatory regions and candidate genes associated with backfat thickness and intramuscular fat content traits in Xiang pigs.","authors":"Xia Chen, Yundi Zheng, Fengbin Hu, Xiaoli Liu, Wei Wang, Fenfang Qi, Xi Niu, Shihui Huang, Jiafu Wang, Xueqin Ran","doi":"10.1186/s12864-025-11860-y","DOIUrl":"10.1186/s12864-025-11860-y","url":null,"abstract":"<p><p>Backfat thickness (BFT) and intramuscular fat (IMF) content reflect fat deposition and meat quality in pigs. Numerous genetic variations contribute to differences in BFT and IMF for different pig breeds. However, limited information is available on the genetic variants associated with IMF deposition in Xiang pigs. To identify the putative regulatory regions and candidate genes associated with BFT and IMF traits in Xiang pigs, we integrated the whole genomic DNA genotyping and RNA-sequencing data in Longissimus thoracis muscle from F2 individuals of Large White × Xiang pig cross and performed the expression quantitative trait loci (eQTL) analyses. We identified a total of 64,419 significant cis-variant-eGene, including 33,288 eSNPs, 7,910 eInDels, and 5,940 eSVs. Among them, 1,156 cis-eQTL loci overlapped with QTL for IMF and BFT, affecting the expressions of 541 genes, including 54 transcription factors. Enrichment analysis revealed that key candidate genes were significantly associated with lipid metabolism pathways, such as mTOR and PPAR signaling. Overlap analysis demonstrated that several eQTLs exhibited dual regulatory effects on gene expression. Notable eQTL hotspots included eSNP 12:52760182_T, eInDel 2:6807484-6,807,485, and three eSV sites, with the P2RY6 gene significantly associated with multiple variants. Our results indicated that many regions across the pig genome that affected gene expression level (eQTL) and overlapped with QTL regions associated with the fat store and lipid metabolism for IMF and BFT. These findings enhance our understanding of the genetic mechanisms underlying fat deposition in Xiang pigs and provide a theoretical framework for future functional studies and genomic selection.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"733"},"PeriodicalIF":3.7,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12333138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798114","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":"BvHP4b gene in red beet promotes tuber enlargement and enhances resistance to Pst DC3000.","authors":"Xiaozheng Xing, Zengyuan Tian, Shuran Yang, Xiaomin Wang, Zhiyang Xing, Di Wu, Shuting Zheng, Yuqi Guo","doi":"10.1186/s12864-025-11864-8","DOIUrl":"10.1186/s12864-025-11864-8","url":null,"abstract":"<p><p>One important component of the cytokinin signaling pathway is the histidine phosphotransferase (HP), which plays an essential role in regulating downstream gene expression by transferring phosphate groups. The role of histidine phosphotransfer proteins (HPs) in sugar beets under abiotic and biotic stresses remains unclear. The results showed that the expression of BvHP4b in red beets increased in response to the exogenous hormone 6-BA. Transgenic Arabidopsis seedlings with heterologous expression of BvHP4 T3 lines (BvHP4-OE) displayed enhanced growth and resistance to Pst DC3000. Moreover, the expression of NPR1 and PRs was increased in the T3 transgenic lines compared to the control. Subcellular localization analysis revealed that BvHP4b primarily localized to the cell membrane. Transgenic red beets overexpressing BvHP4b (BvHP4b-OX lines) and bvhp4b mutant plants (KO lines) using CRISPR/Cas9 technology were generated respectively. The BvHP4b-OX lines showed enhanced taproot development, which was attributed to the altered expression of BvXTH33, BvCESA6, BvCDC2, and BvCEL1 genes. These lines also exhibited increased tolerance to Pst DC3000 by regulating synthesis of SA and modulating the expression of genes involved in plant immunity. In contrast, the KO plants were more susceptible to Pst DC3000 compared to the control plants. Furthermore, BvHP4b was shown to interact with BvCDC2 both in vivo and in vitro. Overall, this study suggests that the BvHP4b protein acts as a positive regulator, enhancing taproot enlargement and tolerance to Pst DC3000 in sugar beet plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"731"},"PeriodicalIF":3.7,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798113","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":"An optimized protocol for in vitro regeneration and genetic transformation of broomcorn millet.","authors":"Zhaolan Cui, Wenmin Wei, Xinqi Han, Yuechen Wang, Juqing Jia, Haigang Wang, Longlong Liu, Lun Wang, Ayesha Tassawark, Jun Li, Dongming Li, Yuxiang Wu, Li Zhang","doi":"10.1186/s12864-025-11899-x","DOIUrl":"10.1186/s12864-025-11899-x","url":null,"abstract":"<p><strong>Background: </strong>Abiotic stress has been a great challenge to global food security. To reduce its effects, breeding crops for tolerance to abiotic stresses is a promising strategy. Broomcorn millet is cultivated in arid and semiarid areas with a high degree of abiotic stress tolerance. However, due to the lack of efficient genetic transformation methods for broomcorn millet, the characterization of genes related to abiotic stress tolerance lags behind that of other crop species. Therefore, establishing efficient in vitro regeneration and genetic transformation methods for broomcorn millet is essential.</p><p><strong>Results: </strong>In this study, we used mature seeds of the sequenced variety 'Longmi 4' as explants and optimized its in vitro regeneration and genetic transformation methods. The optimal hormone concentrations for embryogenic callus induction medium were 2.5 mg/L 2,4-dichlorophenoxyacetic and 0.5 mg/L 6-benzylaminopurine. The optimal hormone concentrations for shoot regeneration medium were 2 mg/L 6-benzylaminopurine and 0.5 mg/L a-naphthaleneacetic acid. Additionally, the co-cultivation time was 3 days, and the optimal hygromycin concentration for putative transgenic callus selection was 20 mg/L. The transformation efficiency was 21.25% after our modification approach.</p><p><strong>Conclusions: </strong>Here, we present a simple and highly efficient Agrobacterium-mediated genetic transformation protocol for broomcorn millet. Our work provides a tool for the characterization of genes related to important traits, as well as a new strategy for broomcorn millet breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"725"},"PeriodicalIF":3.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793402","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":"Characterization and comparative analysis of the complete mitochondrial genome of Phlomoides rotata, a traditional Tibetan medicinal plant.","authors":"Houzhou Liu, Zhongqiong Tian, Tsering Danzin, Xin Tan, Junwei Wang, Qiong La, Wei Li","doi":"10.1186/s12864-025-11871-9","DOIUrl":"10.1186/s12864-025-11871-9","url":null,"abstract":"<p><strong>Background: </strong>Phlomoides rotata, an endemic Tibetan medicinal plant adapted to extreme alpine environments, faces conservation challenges due to habitat degradation and overharvesting. Despite its ecological and medicinal importance, its mitochondrial genome remains uncharacterized, limiting insights into its evolutionary adaptations and genomic architecture.</p><p><strong>Results: </strong>We present the initial de novo assembly and annotation of the P. rotata mitochondrial genome, a circular molecule with a GC content of 45.06% and a length of 377,312 bp. A total of 32 protein-coding genes (PCGs), three ribosomal RNA (rRNA) genes, and 12 transfer RNA (tRNA) genes were identified through genome annotation. These genes include multicopy genes (trnM-CAU, matR). Analysis of codon usage bias indicated a preference for A/U ending synonymous codons, aligning with trends observed in other angiosperms. RNA editing research revealed 445 C-to-U transitions, predominantly at the second codon position, with nonsynonymous alterations (71%) surpassing synonymous changes, indicating potential functional adaptive roles. Repetitive sequence analysis uncovered 81 simple sequence repeats (SSRs) and a large palindromic repeat (13,075 bp), linked to genomic rearrangements. Homologous alignments identified 12 chloroplast-derived fragments in the mitogenome, including intact tRNA and rpl23 genes, evidencing interorganellar gene transfer. Phylogenetic analysis using 27 conserved PCGs positioned P. rotata within a well-supported Lamiales clade, closely related to Leonurus japonicus, corroborating its taxonomic placement and providing a framework for evolutionary studies.</p><p><strong>Conclusions: </strong>The P. rotata mitogenome exhibits structural complexity and adaptive features, including codon bias, RNA editing, and repetitive sequences, underscoring its role in high-altitude adaptation. These findings provide critical genomic resources for conservation, breeding, and understanding the molecular mechanisms of organellar evolution in extreme environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"727"},"PeriodicalIF":3.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793403","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":"Determination of high-confidence germline genetic variants in next-generation sequencing through machine learning models: an approach to reduce the burden of orthogonal confirmation.","authors":"Muqing Yan, Qiandong Zeng, Zhenxi Zhang, Patricia Okamoto, Stanley Letovsky, Angela Kenyon, Natalia Leach, Jennifer Reiner","doi":"10.1186/s12864-025-11889-z","DOIUrl":"10.1186/s12864-025-11889-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"728"},"PeriodicalIF":3.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12326712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793405","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}