BMC Genomics最新文献

{"title":"Transcriptomic analysis demonstrates moderators of muscle quality are altered in age-related sarcopenic obesity.","authors":"Eleanor R Schrems, Ana Regina Cabrera, Ronald G Jones, Francielly Morena, Kevin A Murach, Nicholas P Greene, Tyrone A Washington","doi":"10.1186/s12864-025-12080-0","DOIUrl":"10.1186/s12864-025-12080-0","url":null,"abstract":"<p><strong>Background: </strong>Sarcopenic obesity (SO) is the combined condition of sarcopenia and obesity, which commonly occurs in the older adult population. SO is associated with poor physical function, increased risk of musculoskeletal injury, and reduced quality of life and independence. Information on the molecular underpinnings of this condition is limited. The aim of this study was to provide a transcriptomic analysis characterizing SO induced by lifelong obesity and to provide a deeper understanding of the etiology of the condition.</p><p><strong>Results: </strong>Young (Y) (6 mo) and aged (A) (21-24 mo) mice were fed either normal chow (L) (12% kcal from fat) or high-fat (O) (60% kcal from fat) diets ad libitum. Through multiple analyses, we observed that genes related to ECM remodeling were downregulated in AO compared with YO, providing insight into the effects of age in a life-long obese condition. Furthermore, we observed that genes related to contraction in slow-twitch muscle fibers and fast-to-slow muscle fiber type transitions were upregulated with obesity in the aged condition.</p><p><strong>Conclusion: </strong>Taken together, our findings reveal specific pathways of dysregulation in SO skeletal muscle, offering molecular insights that enhance our understanding of the underlying mechanisms contributing to impaired muscle function in this condition. Further exploration of these dysregulations is critical to identifying therapeutic treatments targeting the source of muscle functional impairment in SO.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"898"},"PeriodicalIF":3.7,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12513022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257242","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 predictions for growth and feed efficiency traits in a duck breeding population.","authors":"Wentao Cai, Chengming Han, Linxi Zhu, Mengdie Wang, Qinglei Yang, Zhenlin Liu, Zhengkui Zhou, Jian Hu, Shuisheng Hou","doi":"10.1186/s12864-025-12087-7","DOIUrl":"10.1186/s12864-025-12087-7","url":null,"abstract":"<p><strong>Background: </strong>In the commercial broiler duck industry, optimizing breeding practices is crucial, especially for growth and feed efficiency traits. Although genomic selection (GS) has been successfully applied in livestock, its use in duck breeding is not yet widespread. This study aims to investigate genetic parameters and refine GS strategies for feed efficiency and growth traits in ducks, paving the way for more precise and efficient breeding programs.</p><p><strong>Results: </strong>We investigated genetic parameters of 12 growth and feed efficiency traits in a commercial breeding Line of 52,610 ducks across 10 generations. We applied genomic predictions to 2779 ducks from the latest three generations. Heritability of these traits ranging from 0.16 to 0.51. Genomic prediction accuracy was higher for GBLUP under cross-validation than forward validation. This performance discrepancy was influenced by reference population recency and trait complexity. Notably, single-step GBLUP consistently outperformed pedigree-based BLUP, particularly for feed efficiency traits. Expanding the reference population with recent generations improved forward validation accuracy by 27.7%, highlighting the critical role of updated genetic data in enhancing across-generation predictive accuracy. The newly proposed residual feed intake adjusted for breast muscle volume demonstrated a higher heritability and predictive accuracy compared to its predecessor. Pruning variants using Linkage disequilibrium thresholds of 0.075 resulted in an increase of 0.05 in the average predictive accuracy. Similarly, omitting the Hardy-Weinberg equilibrium threshold generally resulted in higher predictive accuracy for most traits. However, for traits such as BMW, BMT, and BMV, we observed enhanced predictive accuracy when applying a specific threshold for HWE test pruning. The BayesRC model, when informed by cis-eQTLs or their regulated genes, particularly from adipose and muscle tissues, increased predictive accuracy for various traits, highlighting the importance of integrating biological data into genomic prediction frameworks.</p><p><strong>Conclusions: </strong>This study offers encouraging evidence for utilizing GS to enhance growth and feed efficiency traits in ducks. It offers valuable insights into optimizing GS for duck breeding, emphasizing the critical roles of model selection, marker density refinement, and the strategic integration of prior biological information.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"894"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249549","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 genomic analysis of Mycoplasma pneumoniae isolated in the United Kingdom, between 2016 and 2024.","authors":"Rediat Tewolde, Joshua C D'Aeth, Rebecca Thombre, Michael L Beeton, Richard S Rowlands, Samuel K Sheppard, Matthew D Hitchings, Ben Pascoe, Victoria J Chalker, Baharak Afshar","doi":"10.1186/s12864-025-12101-y","DOIUrl":"10.1186/s12864-025-12101-y","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Mycoplasma pneumoniae is a bacterium that causes upper and lower respiratory infections in children and adults. Epidemics occur over the winter period every few years with the most recent seen in 2023/24. These epidemics are thought to be due to the circulation of p1 type variants of M. pneumoniae which have cyclic epidemiology, with the peaks of infection driven by naïve individuals, mainly those &lt; 5-years-old. Currently there is no routine monitoring or genomic surveillance to detect variants of M. pneumoniae circulating in the UK. We analysed 38 genomes of M. pneumoniae isolated in the UK between 2016 and 2024 for the detection of Macrolide-resistant M. pneumoniae (MRMP) and typing of M. pneumoniae variants. Core-genome analysis was used to compare the M. pneumoniae UK data with the global genomic data of 290 M. pneumoniae strains from 14 countries.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Of the 38 isolates from UK, the majority were obtained from male patients (62%), with the most common age range (38%) being the 0-15 years age group. All 38 UK isolates were identified as M. pneumoniae, of which 19 isolates (50%) were identified as p1-type 1 strains, and 19 isolates (50%) as p1-type 2. Of 38 isolates, six (16%) isolates were MRMP, of which four (67%) MRMP isolates were identified as sequence type (ST)3 from 2024 and the remaining two MRMP isolates from 2016 to 2024 were identified as ST14. Two core-genome phylogenetic trees; one based on strains from UK only (38 strains) and the other on a combined dataset of global and UK strains (328 strains), revealed two main clades corresponding to p1 types (p1-type 1 and p1-type 2 clades). Within these clades, strains were generally grouped into subclades according to their sequence type (ST), with a few exceptions observed in the global dataset. The phylogenetic tree for the 328 strains (290 global data and 38 UK data) showed 7 Subclades: Subclade 1 (ST3), Subclade 2 (mainly ST3/ST20), Subclade 3 (ST17), Subclade 4 (ST1), Subclade 5 (mainly ST14), Subclade 6 (mainly ST7/ST47) and Subclade 7 (ST2). ST3 strains were positioned in two Subclades (Subclade 1 and Subclade 2). 99% of the isolates in Subclade 1 (ST3) were MRMP. ST3 MRMP includes the most predominant strains in East Asia (Taiwan, Korea, Japan and China). Subclade 1 (ST3) was predominant in the strains isolated in 2024 from the UK that were included in this study out of which three ST3 MRMP strains were clustered in Subclade 1. Macrolide resistance was present in all Subclades except Subclade 7 (ST2).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;It is imperative to continuously monitor Subclade 1 in the UK to better understand the burden of macrolide resistance and the potential spread and evolution of this strain within the population. Whole genome sequencing based genomic surveillance of M. pneumoniae is a vital tool for the detection of macrolide resistance, and the surveillance of circulating strains during outbreaks and seaso","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"893"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249530","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":"Morphology, transcriptome and physiology analyses reveal adaptation mechanisms of Gymnocypris Przewalskii juveniles to saline-alkaline stresses.","authors":"Zihan Gao, Le Wang, Yanrong Cui, Yixin Li, Luyang Yan, Yike Deng, Wengen Tian, Fulei Wei, Jian Liang","doi":"10.1186/s12864-025-12054-2","DOIUrl":"10.1186/s12864-025-12054-2","url":null,"abstract":"<p><strong>Background: </strong>Naked carp (Gymnocypris przewalskii), a fish endemic to Qinghai Lake, China, has attracted extensive attention for its adaptation to salinity and alkalinity stress. However, the survival mechanism of G. przewalskii against saline-alkaline water environments remains elusive. In this study, we aimed to reveal the causes of saline-alkaline tolerance of G. przewalskii through the analysis of morphological, physiological and transcriptomic dimensions. The combination of growth performance and physiological indexes, and the morphology of gill tissues and transcriptomics strengthened the connection between this experiment, and further explored and analyzed the causes of salinity tolerance of G. przewalskii.</p><p><strong>Results: </strong>Analysis of growth indices revealed weight gain rate (WGR), specific growth rate (SGR), average daily gain (ADG), and specific growth rate of length (SGRL) were promoted under mild alkaline stress and saline-alkaline stress. The alkalinity of A24.36 (7.80 mmol/L) and a saline-alkalinity of SA23.05 (3.84‰, 7.38 mmol/L) is most favorable for growth. All stresses caused shortened length of gill lamellae and between-lamellae distance. At the same time, stress led to a substantial increase in glycogen content and enhanced fructose-1,6-bisphosphate aldolase (FBA) activity in the liver and muscle. The transcriptome results in gills showed significant enrichment of biological processes such as manganese ion transport in alkaline stress, and reflection of stimuli, immunity, etc. in saline-alkaline stress. In gills, energy metabolism process, PI3K signaling pathway were significantly activated in both alkaline stress and saline-alkaline stress, NF-kappa B signaling pathway was significantly activated downstream of PI3K in alkaline stress; mTOR signaling pathway, MAPK signaling pathway and Rap1 signaling pathway were significantly activated downstream of PI3K under saline-alkaline stress.</p><p><strong>Conclusion: </strong>This study unveiled the changes in growth indices, gill morphology, physiological parameters, and transcriptomics, which facilitated elucidation of the adaption mechanism of G. przewalskii juveniles to alkaline stress and saline-alkaline stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"897"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249552","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":"Developing a core collection for the conservation of Theobroma cacao's genetic diversity.","authors":"Evelyn T Todd, Fabrizio Arigoni, James A Holzwarth, Laurence Bellanger, Patrick Descombes, Eduardo Beche, Tony Lass, Mark J Guiltinan, Siela N Maximova, Mariela Leandro, Virginie Mérot, Maud Lepelley, Audrey Fillodeau","doi":"10.1186/s12864-025-11882-6","DOIUrl":"10.1186/s12864-025-11882-6","url":null,"abstract":"<p><strong>Background: </strong>Crop core collections serve as a means of conserving genetic variation and providing a diverse array of accessions for future research and breeding endeavours. Despite the challenges posed by diseases and climate change to global cacao production, no centralized core collection currently exists. To address this gap, we have assembled a new, general-purpose cacao core collection from accessions present in international collections.</p><p><strong>Results: </strong>A dataset of 310 cacao accessions from international collections were selected based on material availability, geographic origin, and known phenotypic characteristics. Population structure analysis of 26,601 single nucleotide polymorphisms (SNPs) from these accessions revealed ten distinct genetic groups, consistent with previous studies. A core collection of 96 accessions was subsequently selected, encompassing 99.6% of the genetic diversity within the dataset. This collection comprises representatives of all ten genetic groups, as well as accessions exhibiting high productivity and pathogen resistance.</p><p><strong>Conclusions: </strong>This core collection will serve as a crucial genetic resource for the cacao community. Cultivating and maintaining the plants from this core collection will contribute to the preservation of genetic diversity within the population. Furthermore, this collection, when combined with appropriate phenotyping, will establish a foundation for novel breeding programs aimed at enhancing crop improvement in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"896"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249559","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 and evolution of the plant sulfotransferase family.","authors":"Shuangxin Han, Zhujun Chen, Quanlong Liu, Yueying Ding, Jia Wang, Hongbo Liu, Junyang Zou, Zhiying Hong, Hongmei Zhang, Wenping Yang, Lan Zhang, Hongwei Liu, Min Yuan","doi":"10.1186/s12864-025-12117-4","DOIUrl":"10.1186/s12864-025-12117-4","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"895"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249594","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":"The two sub-genomes of the allotetraploid frog Xenopus laevis are evolving under similar selective pressure in extant populations.","authors":"Dareen Almojil, Vinu Manikandan, Nizar Drou, John Measey, Stéphane Boissinot","doi":"10.1186/s12864-025-12036-4","DOIUrl":"10.1186/s12864-025-12036-4","url":null,"abstract":"<p><p>The model species Xenopus laevis is an allotetraploid species, whose genome consists of two sub-genomes (the L and S sub-genomes) that were inherited from its parental species. Previous studies comparing the genome of X. laevis with other species of the genus revealed that the L sub-genome was more conserved than the S sub-genome suggesting it has been evolving under stronger purifying selection. However, it remains unclear if this difference reflects evolutionary processes that are still at play in extant populations. To answer this question, we conducted the first genome-wide survey of variation in this species by re-sequencing 44 individuals from its native South African range at ~ 10 × coverage. We generated a dataset of ~ 260M SNPs, which constitutes a valuable resource for the Xenopus community. We found that the South African populations of X. laevis are highly structured and differentiated, reflecting ancient divergence followed by more recent admixture at contact zones. We also determined that the landscapes of variation of the L and S sub-genomes do not show any significant differences suggesting that the two sub-genomes are responding to evolutionary forces in a similar manner. In particular we showed that purifying selection and positive selection are acting identically on the two sub-genomes, suggesting that the sub-genomes of X. laevis are evolving under similar selective pressure. Since 60% of the ancestral homeologous genes have been retained in X. laevis, this result suggests that the function of those genes is conserved on both sub-genomes or that a large number of genes has experienced neo- or sub-functionalization.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"887"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243805","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":"Genetic architecture of the Sindhi Indian population: a 19X-STR forensic analysis.","authors":"Khushboo Gautam, Chanchal Devnani, Shruti Dasgupta, Madhusudan Reddy Nandineni, Kumarasamy Thangaraj, Gyaneshwer Chaubey, Rakesh Rawal","doi":"10.1186/s12864-025-12032-8","DOIUrl":"10.1186/s12864-025-12032-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"889"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243797","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":"Transcriptome analysis of five-toed jerboa organs reveals high-altitude adaptation mechanisms.","authors":"Shan-Shan Sun, Hao-Ting Zhang, Hai-Wen Yan, Xiao-Yu Kang, Qi-Qige Buren, Qian-Cheng Wang, Ming Ming, Jie-Ru Feng, Na Zhu, Xin Li, Yu Ling, Dong Zhang, Xiao-Dong Wu, Shuai Yuan, He-Ping Fu","doi":"10.1186/s12864-025-12096-6","DOIUrl":"10.1186/s12864-025-12096-6","url":null,"abstract":"<p><p>High-altitude environments are characterised by extreme conditions, including hypoxia, low temperatures, and intense ultraviolet radiation. Mammals inhabiting these environments have evolved unique adaptive mechanisms, the study of which elucidates survival strategies and evolutionary pathways under extreme conditions. Understanding how native high-altitude animals respond to such environments is highly important. This study investigated the high-altitude adaptation mechanisms of the five-toed jerboa (Orientallactaga sibirica) distributed in Qinghai Province (4229 m) and Hebei Province (498 m), China, through comparative transcriptomic analysis of heart, lung, and kidney tissues. The results revealed greater mRNA transcriptional differences in the lung tissue than in the heart and kidney tissues of high-altitude jerboas, indicating heightened lung sensitivity to high-altitude conditions. In lung tissue, high-altitude jerboas show differential expression of genes related to the Complement and Coagulation cascades, Heme binding, Oxidation-reduction process (such as MASP1, A2M, SERPING1, CD55, FGA, C5AR1, and KNG1), which may be associated with modulating immune functions to mitigate hypobaric hypoxia, intense radiation, and cold-induced damage and reducing thrombosis and inflammation risks. Heart tissue exhibits differential expression of Oxidative phosphorylation and Lipid metabolism genes (such as NDUFC2, NDUFA3, NDUFS4, COX4I2, PAFAH1B3, SGMS2 and PPAR2B), which may help maintain energy equilibrium under hypoxic and cold challenges. Kidney tissue exhibits differential enrichment of pathways such as arachidonic acid metabolism and steroid hormone biosynthesis mediated by genes including CYP4A11, CYP2C29, GPX2, PTGDS, CBR1, and UGT2B31, which may help coordinate vascular regulation, immune response, and oxidative balance to maintain systemic homeostasis. These pathways and genes are differentially enriched and expressed between high-altitude and low-altitude five-toed jerboas, which may be candidates for further functional studies of plateau environmental adaptability. Our findings provide candidate genes and pathways for intraspecies adaptations across microenvironments and highlight the need for further functional validation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"888"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243760","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":"Lineage-specific expansions of the Dicer gene family in tardigrades.","authors":"Bethany Weinberg, Teresa W Lee, Natalie C Steinel, Frédéric J J Chain","doi":"10.1186/s12864-025-12050-6","DOIUrl":"10.1186/s12864-025-12050-6","url":null,"abstract":"<p><strong>Background: </strong>RNA interference (RNAi) is an important pathway for gene regulation and immunity. Dicer is a conserved RNAi pathway protein that is found in eukaryotes, with many species expressing multiple dicer gene copies. However, there remains entire lineages such as the phylum Tardigrada with little information about the presence and diversity of dicer genes, limiting our understanding of the evolution and diverse functions of dicer. Our study sought to understand dicer evolution in tardigrades and its phylogenetic relationship to other invertebrate dicers, including the dicer gene duplication in arthropods.</p><p><strong>Results: </strong>Comparative genomic analyses with ten tardigrade species revealed an expansion of dicer genes in tardigrades. The eight Eutardigrades investigated - Hypsibius exemplaris, Ramazzottius varieornatus, Paramacrobiotus metropolitanus, P. fairbanksi, P. richtersi, Richtersius cf. coronifer, Acutuncus antarcticus and Milnesium tardigradum - and two Heterotardigrades Echiniscoides cf. sigismundi and Echiniscus testudo each contain two to four copies of dicer in their genome. Our results are consistent with a Dicer duplication in the common ancestor of Tardigrada and Arthropoda, followed by lineage-specific duplications that form a sister clade to the arthropod Dicer-2. The tardigrade Dicers contain canonical conserved domains including helicase, PAZ, and RNase III, and their domain-specific phylogenetic diversification suggests functional differentiation after duplication, especially for helicase.</p><p><strong>Conclusions: </strong>Our study identified multiple distinct tardigrade-specific dicer duplications following an ancient duplication that is shared in both Eutardigrades and Heterotardigrades. Phylogenetic analyses are consistent with a Dicer duplication before the split of Tardigrada and Arthropoda that led to Dicer-2, which also groups with duplications found in Kinorhyncha and Platyhelminthes. Our study provides insights into Dicer evolution in Tardigrada by characterizing dicer duplications and divergence across various lineages.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"891"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243767","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}