BMC Genomics最新文献

{"title":"TransGeneSelector: using a transformer approach to mine key genes from small transcriptomic datasets in plant responses to various environments.","authors":"Kerui Huang, Jianhong Tian, Lei Sun, Haoliang Hu, Xuebin Huang, Shiqi Zhou, Aihua Deng, Zhibo Zhou, Ming Jiang, Guiwu Li, Peng Xie, Yun Wang, Xiaocheng Jiang","doi":"10.1186/s12864-025-11434-y","DOIUrl":"10.1186/s12864-025-11434-y","url":null,"abstract":"<p><p>Gene mining is crucial for understanding the regulatory mechanisms underlying complex biological processes, particularly in plants responding to environmental conditions. Traditional machine learning methods, while useful, often overlook important gene relationships due to their reliance on manual feature selection and limited ability to capture complex inter-gene regulatory dynamics. Deep learning approaches, while powerful, are often unsuitable for small sample sizes. This study introduces TransGeneSelector, the first deep learning framework specifically designed for mining key genes from small transcriptomic datasets. By integrating a Wasserstein Generative Adversarial Network with Gradient Penalty (WGAN-GP) for sample generation and a Transformer-based network for classification, TransGeneSelector efficiently addresses the challenges of small-sample transcriptomic data, capturing both global gene regulatory interactions and specific biological processes. Evaluated in Arabidopsis thaliana, the model achieved high classification accuracy in predicting seed germination and heat stress conditions, outperforming traditional methods like Random Forest and Support Vector Machines (SVM). Moreover, Shapley Additive Explanations (SHAP) analysis and gene regulatory network construction revealed that TransGeneSelector effectively identified genes that appear to have upstream regulatory functions based on our analyses, enriching them in multiple key pathways which are critical for seed germination and heat stress response. RT-qPCR validation further confirmed the model's gene selection accuracy, demonstrating consistent expression patterns across varying germination conditions. The findings underscore the potential of TransGeneSelector as a robust tool for gene mining, offering deeper insights into gene regulation and organism adaptation under diverse environmental conditions. This work provides a framework that leverages deep learning for key gene identification in small transcriptomic datasets.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"259"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647189","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 identification and expression analysis of TaFDL gene family responded to vernalization in wheat (Triticum aestivum L.).","authors":"Wenjie Kan, Yameng Gao, Yan Zhu, Ziqi Wang, Zhu Yang, Yuan Cheng, Jianjun Guo, Dacheng Wang, Caiguo Tang, Lifang Wu","doi":"10.1186/s12864-025-11436-w","DOIUrl":"10.1186/s12864-025-11436-w","url":null,"abstract":"<p><strong>Background: </strong>FLOWERING LOCUS D (FD) is a basic leucine zipper (bZIP) transcription factor known to be crucial in vernalization, flowering, and stress response across a variety of plants, including biennial and winter annual species. The TaFD-like (TaFDL) gene in wheat is the functional homologue of Arabidopsis FD, yet research on the TaFDL gene family in wheat is still lacking.</p><p><strong>Results: </strong>In this study, a total of 62 TaFDL gene family members were identified and classified into 4 main subfamilies, and these genes were located on 21 chromosomes. A comprehensive analysis of the basic physicochemical properties, gene structure, conservation motif, conserved domain, and advanced protein structure of TaFDL gene family revealed the conservation among its individual subfamily. The family members underwent purifying selection. The segmental duplication events were the main driving force behind the expansion of the TaFDL gene family. The TaFDL gene family underwent differentiation in the evolution of FD genes. Additionally, the subcellular localization and transcriptional activation activities of five key TaFDL members were demonstrated. Gene Ontology (GO) annotations and promoter cis-regulatory element analysis indicated that the TaFDL members may play potential roles in regulating flowering, hormone response, low-temperature response, light response, and stress response, which were verified by transcriptome data analysis. Specifically, quantitative real-time PCR (qRT-PCR) analysis revealed that five TaFDL genes exhibited differential responses to different vernalization conditions in winter wheat seeding. Finally, the homologous genes of the five key TaFDL genes across nine different wheat cultivars highlight significant genetic diversity.</p><p><strong>Conclusion: </strong>These findings enrich the research on FD and its homologous genes, providing valuable insights into the TaFDL gene family's response to vernalization.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"255"},"PeriodicalIF":3.5,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647170","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":"Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element.","authors":"Jessica Castellanos-Labarcena, Yoamel Milián-García, Tyler A Elliott, Dirk Steinke, Robert Hanner, Sarah J Adamowicz","doi":"10.1186/s12864-025-11449-5","DOIUrl":"10.1186/s12864-025-11449-5","url":null,"abstract":"<p><strong>Background: </strong>Advancing our knowledge of vector species genomes is a key step in our battle against the spread of diseases. Biting midges of the genus Culicoides are vectors of arboviruses that significantly affect livestock worldwide. Culicoides stellifer is a suspected vector with a wide range distribution in North America, for which cryptic diversity has been described.</p><p><strong>Results: </strong>With just one specimen of C. stellifer, we assembled and annotated the nuclear and mitochondrial genome using the ultra-low input DNA PacBio protocol. The genome assembly is 119 Mb in length with a contig N50 value of 479.3 kb, contains 11% repeat sequences and 18,895 annotated protein-coding genes. To further elucidate the role of this species as a vector, we provide genomic evidence of a non-retroviral endogenous viral element integrated into the genome that corresponds to rhabdovirus nucleocapsid proteins, the same family as the vesicular stomatitis virus.</p><p><strong>Conclusions: </strong>This genomic information will pave the way for future investigations into this species's putative vector role. We also demonstrate the practicability of completing genomic studies in small dipterans using single specimens preserved in ethanol as well as introduce a workflow for data analysis that considers the challenges of insect genome assembly.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"247"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633408","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 transcriptome analysis in oviduct provides insight into microRNAs and ceRNA regulative networks that targeted reproduction of goat (Capra hircus).","authors":"Qingqing Liu, Zhipeng Sun, Yufang Liu, Xiaoyun He, Chunhuan Ren, Xiangyu Wang, Ran Di, Yongju Zhao, Zijun Zhang, Mingxing Chu","doi":"10.1186/s12864-025-11438-8","DOIUrl":"10.1186/s12864-025-11438-8","url":null,"abstract":"<p><strong>Background: </strong>Reproduction traits are crucial for livestock breeding and represent key economic indicators in the domestic goat (Capra hircus) industry. The oviduct, a critical organ in female mammals, plays a pivotal role in several reproductive processes; however, its molecular mechanisms remain largely unknown. Non-coding RNA and mRNAs are essential regulatory elements in reproductive processes; yet their specific roles and regulatory networks in goat oviducts remain unclear.</p><p><strong>Results: </strong>In this study, we conducted small RNA sequencing of the oviduct in high- and low-fecundity goats during the follicular (FH and FL groups, n = 10) and luteal (LH and LL groups, n = 10) phase, profiling 20 tissue samples. Combinatorial whole-transcriptome expression profiles were applied to the same samples to uncover the competitive endogenous RNA (ceRNA) regulation network associated with goat fecundity. RT-qPCR was employed to validate the miRNA profiling results, and ceRNA regulatory networks were analyzed through luciferase assay. Gene set enrichment analysis (GSEA) confirmed that the cytokine-cytokine receptor interaction and TGF-β signaling pathway, both related to embryonic development, were enriched in DEM target genes. Additionally, miR-328-3p, a core miRNA, targets SMAD3 and BOP1, which are involved in the negative regulation of cell growth and embryonic development. TOB1 and TOB2, targeted by miR-204-3p, regulate cell proliferation via the protein kinase C-activating G-protein coupled receptor signaling pathway. Analyses of ceRNA regulatory networks revealed that LNC_005981 - miR-328-3p - SMAD3 and circ_0021923 - miR-204-3p - DOT1L may affect goats' reproduction, findings that were validated using luciferase assay.</p><p><strong>Conclusion: </strong>Analysis of whole-transcriptome profiling of goat oviducts identified several key miRNAs and ceRNAs that may regulate oocyte maturation, embryo development, and the interactions between the oviduct and gametes/early embryos, providing insights into the molecular mechanisms of reproductive regulatory networks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"250"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633467","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":"Comparative genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments.","authors":"Yuntong Du, Changhua He, Karen G Lloyd, Tatiana A Vishnivetskaya, Hongpeng Cui, Bing Li, Da Gong, Xiaopeng Fan, Dayi Zhang, Hongchen Jiang, Renxing Liang","doi":"10.1186/s12864-025-11410-6","DOIUrl":"10.1186/s12864-025-11410-6","url":null,"abstract":"<p><strong>Background: </strong>Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level.</p><p><strong>Results: </strong>A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade ('polar group' hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas. Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions.</p><p><strong>Conclusions: </strong>The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"248"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633423","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 Valine-Glutamine gene family in Chenopodium quinoa Willd and analysis of its expression pattern and subcellular localization under drought stress.","authors":"Dongfang Zhang, Xiaolin Zhu, Xuefen Du, Xian Wang, Baoqiang Wang, Xiaohong Wei","doi":"10.1186/s12864-025-11313-6","DOIUrl":"10.1186/s12864-025-11313-6","url":null,"abstract":"<p><strong>Background: </strong>Chenopodium quinoa Willd (Quinoa) is highly tolerant to drought, cold, and salt stress. Gene editing technology development, and research on quinoa's drought resistance have attracted much attention. The transcriptional cofactor VQ plays an important role in the drought response in plants, but its role in quinoa has not been reported.</p><p><strong>Results: </strong>Bioinformatics identified 23 members of the quinoa VQ gene family, mainly located in the nucleus and unevenly distributed on 10 chromosomes. Gene structure and phylogenetic analysis indicated that the VQ genes were closely related and highly conserved, forming three subfamilies. The cis-acting elements of the promoter reveal its involvement in the response to light and hormonal stress. qRT-PCR analysis showed that all VQ genes were differentially expressed under drought stress, among which CqVQ13 was significantly up-regulated, and subcellular localization indicated that it was localized to the nucleus.</p><p><strong>Conclusion: </strong>This study conducted a systematic bioinformatics analysis of the basic physicochemical properties and chromosome localization of 23 members of the CqVQ gene family. Combined with transcriptome gene expression profiling and qRT-PCR, we found that CqVQ13 was significantly up-regulated under drought stress and localized in the nucleus. This discovery provides an important candidate gene for drought response studies in quinoa and lays the foundation for further exploration of the molecular mechanisms of the VQ gene family in response to drought stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"252"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633439","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":"Exploration of non-coding RNAs related to intramuscular fat deposition Xinjiang Brown cattle and Angus × Wagyu cattle.","authors":"Yuxin Zhou, Wanping Ren, Wei Shao, Yu Gao, Kangyu Yao, Min Yang, Xinyu Zhang, Yiran Wang, Fengming Li, Liang Yang","doi":"10.1186/s12864-025-11453-9","DOIUrl":"10.1186/s12864-025-11453-9","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Non-coding RNAs (ncRNAs) serve as crucial regulatory elements in the process of adipogenesis in animals; however, the specific roles and interrelationships of ncRNAs in bovine fat deposition remain poorly understood. This study aims to investigate the differentially expressed ncRNAs in the longissimus dorsi muscle of Xinjiang Brown cattle (XB) and Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle (AW), to elucidate the regulatory mechanisms underlying lipidogenesis that may involve ncRNAs. Four Xinjiang Brown cattle and four Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle were selected, ensuring they are subjected to identical feeding conditions, in order to evaluate the intermuscular fat (IMF) of longissimus dorsi muscles. The fat content of muscle tissue was quantified using the Soxhlet extraction method, revealing that the fat levels in the AW group were significantly elevated compared to those in the XB group. Taking muscle samples for paraffin sectioning and observing their morphology, it was found that the fat richness of the AW group was significantly higher than that of the XB group. Utilizing high-throughput RNA sequencing technology, we conducted an extensive transcriptomic analysis of longissimus dorsi muscles of XB and AW to identify significant ncRNAs implicated in fat metabolism and adipogenesis. The miRNA analysis yielded between 109,343,831 117,258,570 clean reads, whereas the lncRNA and circRNA analyses produced between 81,607,756 102,917,174 clean reads. Subsequent analysis revealed the identification of 53 differentially expressed miRNAs, 176 differentially expressed lncRNAs, and 234 differentially expressed circRNAs. KEGG enrichment analysis revealed that the target genes of differentially expressed miRNAs, lncRNAs, and circRNAs are significantly enriched in 2, 17, and 22 distinct pathways, respectively. The pathways associated with the differential enrichment of miRNA target genes involve processes such as phosphorylation and protein modification. Concurrently, the pathways linked to the varying enrichment of lncRNA target genes encompass G protein-coupled receptor signaling, regulation of cell death and apoptosis, activities related to GTPase activation, and functions governing nucleotide triphosphatases, among others. The circRNA exhibiting differential expression are significantly enriched in a variety of biological processes, including signal transduction, nucleic acid synthesis, cellular architecture, GTPase activation, and phosphatase activities, among others. The analysis of the ncRNA interaction network suggests that AGBL1, THRB, and S100A13 may play pivotal roles in the formation and adipogenic differentiation of adipocytes. In conclusion, we conducted a comprehensive analysis and discussion of the complete transcriptome of intermuscular fat tissue from the longissimus dorsi muscles in Xinjiang Brown cattle and Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle. This study provides a theoretical foundation for enhancing our unders","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"249"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633436","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 near-complete genome assembly of Fragaria iinumae.","authors":"Haiyuan Du, Yiying He, Maoxian Chen, Xu Zheng, Daping Gui, Jixing Tang, Yu Fang, Yiwei Huang, Hong Wan, Jiwei Ruan, Xin Jin, Andan Zhu","doi":"10.1186/s12864-025-11440-0","DOIUrl":"10.1186/s12864-025-11440-0","url":null,"abstract":"<p><p>Fragaria iinumae, a diploid progenitor species of octoploid strawberries, likely occupies a basal position within the genus Fragaria. In this study, we report a near-complete genome assembly of F. iinumae v2.0, totaling 241.14 Mb with a contig N50 of 33.31 Mb. We identified 14 telomeric and 7 centromeric regions across its seven chromosomes. Compared to previous assemblies, F. iinumae v2.0 demonstrates substantial improvements in both genome continuity (gaps reduced from 29 to 0) and annotation completeness, including the annotation of 4,144 new genes and 395 new gene clusters. Notably, several large structural variants were identified between the F. iinumae v1.0 and F. iinumae v2.0 genomes, with most gaps in the v1.0 assembly overlapping with structural variant breakpoints. Additionally, we found a significant expansion of telomeric repeats in the B subgenome of octoploid strawberries compared to F. iinumae. Interestingly, two telomeres consistently exhibited low repeat abundance in both the diploid and octoploid B subgenomes, suggesting significant contraction early in the evolution of F. iinumae. Furthermore, through multiple lines of genomic evidence-including phylogenetic analyses, genetic distance matrices, a burst of LTR insertions, and the distribution of NLR resistance genes, we conclude that F. iinumae may represent an early-diverging lineage within the strawberry genus. This updated assembly provides a crucial genomic resource for understanding of the origin and structural dynamics of the strawberry genus and facilitates further exploration of genome-wide consequences of polyploidy.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"253"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633410","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":"Assembly and comparative analysis of the complete mitochondrial genome of Echinacanthus longipes (Acanthaceae), endemic to the Sino-Vietnamese karst flora.","authors":"Chunming Gao, Shu Wang, Yusong Huang, Yunfei Deng","doi":"10.1186/s12864-025-11448-6","DOIUrl":"10.1186/s12864-025-11448-6","url":null,"abstract":"<p><strong>Background: </strong>Echinacanthus longipes is an endemic species in the Sino-Vietnamese karst flora in the family Acanthaceae. It displays distinctive environmental adaptation characteristics in karst regions. Although it provides an important model for understanding the role of limestone karst in speciation and endemism, the mitochondrial genome (mtDNA) of E. longipes has not been fully characterized.</p><p><strong>Results: </strong>Here, the mtDNA of E. longipes was successfully assembled as a complex structure in the form of two small circular and three linear molecules with a total length of 810,200 bp. The annotated results revealed 36 protein-coding genes (PCGs), 22 tRNA genes, and three rRNA genes in this mtDNA. Notably, substantial sequence repeats and more tRNAs translocations from the chloroplast to the mtDNA were identified. Among the PCGs of E. longipes, the majority of 401 RNA editing sites were involved in amino acid transitions to hydrophobic sites. The current phylogenetic analysis based on PCGs revealed the evolution of Lamiales and a close relationship between E. longipes and Avicennia marina. However, comparative analyses, including size, structure, GC contents, and genes, reflected the variation in the mitogenomes within Acanthaceae, and the collinearity analysis confirmed the low level of conservation in the genomes of related species in Lamiales. Moreover, the Ka/Ks analysis revealed that negative selection occurred on most PCGs, with the notable exception of ccmB, which underwent positive selection. Interestingly, the ccmB gene had the most protein editing sites.</p><p><strong>Conclusions: </strong>This study will be invaluable for the mitochondrial study of Acanthaceae. It also provides extensive information for functional genetic and adaptive studies of Echinacanthus in karst regions in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"251"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633417","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":"Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors.","authors":"Martin Danner, Matthias Begemann, Florian Kraft, Miriam Elbracht, Ingo Kurth, Jeremias Krause","doi":"10.1186/s12864-025-11444-w","DOIUrl":"10.1186/s12864-025-11444-w","url":null,"abstract":"<p><p>Understanding the dark genome is a priority task following the complete sequencing of the human genome. Short open reading frames (sORFs) are a group of largely unexplored elements of the dark genome with the potential for being translated into microproteins. The definitive number of coding and regulatory sORFs is not known, however they could account for up to 1-2% of the human genome. This corresponds to an order of magnitude in the range of canonical coding genes. For a few sORFs a clinical relevance has already been demonstrated, but for the majority of potential sORFs the biological function remains unclear. A major limitation in predicting their disease relevance using large-scale genomic data is the fact that no population-level constraint metrics for genetic variants in sORFs are yet available. To overcome this, we used the recently released gnomAD 4.0 dataset and analyzed the constraint of a consensus set of sORFs and their genomic neighbors. We demonstrate that sORFs are mostly embedded into a moderately constrained genomic context, but within the gencode dataset we identified a subset of highly constrained sORFs comparable to highly constrained canonical genes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"254"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633443","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}