BMC Genomics最新文献

{"title":"The Baladi cattle are a genetic sieve for indicine and African-taurine genomic loci with positive effects on adaptation to harsh Mediterranean environments.","authors":"Ariel Shabtay, Morris Soller, Johann Sölkner, Gábor Mészáros, Tad Sonstegard, Emel O Ünal, Heather J Huson, Yuri Utsunomiya, Rotem Agmon, Miri Cohen-Zinder, Alessandro Bagnato, Carlotta Ferrari, Maria G Strillacci, Ehud Lipkin","doi":"10.1186/s12864-026-12895-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12895-5","url":null,"abstract":"<p><strong>Background: </strong>The Mediterranean indigenous Baladi cattle is known for its exceptional adaptability to harsh environment, making it a prime candidate for sustainable grazing systems amid global climate change. This study investigates the ancestors of the Baladi genome, genomic regions under selection, and adaptation mechanisms of Baladi cattle.</p><p><strong>Results: </strong>A unique balanced global admixture of taurine and indicine genomes was found, composed of indicine, European taurine and African taurine ancestors. A total of 103 chromosomal regions with significant local deviation were found, taken as selection signatures. A clear tendency of selection for the indicine and African taurine ancestors at the expense of European taurine was observed. Bioinformatics analysis of the selection signature regions revealed genes candidates by location and function to affect Baladi adaptive selection.</p><p><strong>Conclusions: </strong>The Baladi genome is a unique rich mosaic of three domesticated bovine sub-specie lineages. Thus, the Baladi cattle is a mixture already sieved for adaptation to the harsh Mediterranean climate. These findings emphasize the urgent need for conservation efforts to preserve the genetic diversity and adaptive traits of this valuable, endangered breed.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate imputation of African cattle genomes using a diverse reference panel.","authors":"Said I Ng'ang'a, James A Ward, Stephen J Rossiter, Chris G Faulkes, Katia Bougiouri, Gillian P McHugo, Fenton P D Cotterill, Atunga Nyachieo, Olaf Thalmann, Ivica Medugorac, Stefan Krebs, Tad S Sonstegard, Olivier Hanotte, Daniel G Bradley, Gary Vaughan-Smith, David E MacHugh, Laurent A F Frantz","doi":"10.1186/s12864-026-12818-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12818-4","url":null,"abstract":"<p><strong>Background: </strong>In cattle, most commercial single-nucleotide polymorphism (SNP) genotyping arrays have been shown to be suboptimal for capturing genomic variation in non-European populations, particularly in African cattle. Low-coverage whole-genome sequencing (LCWGS) followed by imputation provides a cost-effective method for genotyping that is more adaptable and can outperform genotyping arrays.</p><p><strong>Results: </strong>Here, we generate a high-quality reference imputation panel representative of the complex ancestries of cattle populations in Africa to enable the deployment of LCWGS. To do so, we generated 116 high-coverage (between 20‒24×) new African cattle genomes, representing most cattle breeds across the continent. We combined this data with publicly available genomes from other regions to build a reference panel that comprised over 3,300 cattle genomes from 133 cattle populations, thus capturing the genetic diversity of domestic cattle across the world. After applying a high filtering step to remove poor genome sequences with very low sequence coverage, we retained 1,882 with an average coverage of 7×. We show that the imputation pipeline implemented, based on this reference panel, provides highly accurate genotypes of common (> 99% accuracy) and rare (> 98% accuracy) variants in genome coverage as low as 0.5×.</p><p><strong>Conclusion: </strong>This panel provides an important new resource for genetic improvement and conservation of African cattle populations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response of DNA methylation and gene expression to light treatments in Norway spruce [Picea abies (L.) Karst.].","authors":"Fangqun OuYang, Jinping Zhang, Ran He, Junhui Wang, Mulualem Tigabu, Jianxun Luo","doi":"10.1186/s12864-026-12877-7","DOIUrl":"https://doi.org/10.1186/s12864-026-12877-7","url":null,"abstract":"<p><p>DNA methylation is important for many developmental processes. Its role in plant's adaptation to light conditions, however, remains unclear. In this study, we examined the DNA methylomes of Norway spruce (Picea abies (L.) Karst.) under different light conditions, a combination of both light intensities (10, and 80 µmolm^-2s^- 1) and light qualities (with or without far-red light). The result showed that both light intensity and quality affected seedling growth, with the former playing a major role. Both light intensity and quality drove genome-wide methylation changes, which varied among cytosine contexts (CG/CHG vs. CHH). The changes in light quality and intensity yielded a similar number of differentially methylated regions (DMRs), but light intensity was a major contributor in gene expression changes. At the genome-wide level, DNA methylation changes showed no consistent correlation with gene expression alterations. However, a subset of genes-particularly those involved in photosynthesis and circadian rhythms-exhibited coordinated methylation and expression changes, suggesting context-specific regulatory links. The findings indicate that DNA methylation may directly modulate photosynthesis and photoperiod genes and trigger an epigenetic memory, which in turn affects growth of Norway spruce seedlings in response to light conditions. In sum, our study provides a global picture of DNA methylation and gene expression under different light conditions in conifers and thus paves a way for future studies of light-directed gene regulation in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative metabolome and transcriptome of different tree size reveal wood formation in Corymbia citriodora.","authors":"Chubiao Wang, Xiang Liu, Zhikang Su, Wenliang He, Yuduan Ou","doi":"10.1186/s12864-026-12886-6","DOIUrl":"https://doi.org/10.1186/s12864-026-12886-6","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Corymbia citriodora wood holds extensive application value; however, due to the cross-pollination nature of C. citriodora and the significant genetic variation among offspring, a phenomenon is observed in plantations where trees with the same parental lineage exhibit varying diameter at breast height (DBH). In this study, we hypothesized that the observed DBH variation reflects two divergent adaptation strategies under winter conditions: smaller trees may exhibit heightened cold sensitivity, activating stress responses and entering early dormancy, whereas larger trees may sustain cambial activity through coordinated regulation of cell-cycle genes and carbohydrate metabolism.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Metabolomics showed large trees enriched in phenolic compounds like picroside I and orientin. Transcriptomics revealed their genes were enriched in cell cycle and phenylalanine/tyrosine metabolism pathways, whereas small trees were enriched in abscisic acid (ABA) pathways. Integrated analysis revealed three patterns of transcript-metabolite coordination: (i) concordant upregulation (e.g., shikimate dehydrogenase (SDH)-shikimic acid), (ii) discordant regulation suggesting post-transcriptional control (raffinose accumulation without raffinose synthase (RFS) upregulation in small trees), and (iii) pathway-level flux redirection (phenylpropanoid pathway). Systematically, during winter, small trees exhibited stress-sensitive signatures, characterized by 9-cis-epoxycarotenoid dioxygenase (NCED), pyrabactin resistance/pyrabactin resistance-like (PYR/PYL), ABA-responsive element binding factor (ABF) upregulation, accumulation of raffinose, and transcriptional shift toward lignification (cinnamyl-alcohol dehydrogenase (CAD), peroxidase upregulation). Conversely, large trees showed molecular profiles indicative of stronger adaptability, with transcriptional signatures consistent with continued cell division (E2F transcription factor 3 (E2F3), mini-chromosome maintenance (MCM2/4/5/6) upregulation), cytoskeletal organization (kinesin KIN12B), and active carbohydrate metabolism (sucrose synthase (SUS), trehalose-6-phosphate phosphatase (TPP), alpha-amylase (AMY) upregulation), accumulating cinnamate and shikimic acid.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study advances understanding of tree growth variation by demonstrating that winter conditions reveal divergent adaptation strategies linked to DBH. The key conceptual advance is the integration of stress signaling, carbon metabolism, and cell-wall regulation into a unified framework where differential dormancy timing explains within-family growth variation. Large trees maintain a permissive growth state through coordinated upregulation of cell-cycle, cytoskeletal, and biosynthetic genes, while small trees exhibit coordinated stress responses that accelerate dormancy. These findings provide species-specific targets for functional validation-including E2F3, KIN12B, and NCED-","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the genetic arsenal of Xanthomonas arboricola: new insights into taxonomic classification, pathogenicity and adaptation beyond the effectorome.","authors":"Renata de A B Assis, Alessandro M Varani, Aidan C Shands, Cintia H D Sagawa, José S L Patané, João C Setubal, Paulo A Zaini, Nalvo F Almeida, Robson F de Souza, Camila C M Garcia, Elena G Orellano, James E Adaskaveg, Abhaya M Dandekar, Leandro M Moreira","doi":"10.1186/s12864-026-12916-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12916-3","url":null,"abstract":"<p><strong>Background: </strong>Xanthomonas arboricola (Xar) is a phytopathogenic bacterial species responsible for economically significant diseases in a wide range of plants, including agricultural, ornamental, and forest species. This study aimed to investigate the genomic basis of host specificity, adaptation, and virulence in Xar through comprehensive comparative genomics.</p><p><strong>Results: </strong>A total of 177 genomes from nine Xar pathovars were analyzed for evolutionary relationships and effector repertoires. From these, 30 genetically diverse genomes were selected for in-depth comparison. Core, unique, and shared genes were identified and functionally annotated, focusing on their potential roles in adaptation and pathogenicity. Nineteen of the genomes were originally misclassified and did not belong to the Xar species. The remaining 158 genomes clustered into three major clades: I (Xar. pv. juglandis), II (Xar. pv. pruni + Xar. pv. corylina), and III (miscellaneous Xar). Clades I and II exhibited high effector diversity, ranging from 38 to 54 genes, with Xar. pv. corylina harboring the most. In contrast, Clade III genomes had significantly fewer effectors, with subclade IIIa containing only 5 and IIIb up to 15. Only one TAL effector was found in nine Xar. pv. corylina strains (with no conserved RVD patterns) and in both Xar. pv. guizotiae strains (up to 31 RVDs identified). Phylogenomic and effectorome analyses revealed potential genomic islands acquired via horizontal gene transfer, encoding metal metabolism genes, type II/IV secretion systems, and DNA modification enzymes. Additionally, several gene losses were observed: 19 genomes lacked flagellar assembly genes, 15 lacked nitrate metabolism genes, and 9 lacked cellulose biosynthesis and secretion genes. In contrast, all genomes possessed a lasso peptide biosynthetic cluster, highlighting recurrent genomic rearrangements through insertions and deletions.</p><p><strong>Conclusions: </strong>This study provides a refined understanding of the genetic diversity and adaptive mechanisms in X. arboricola, emphasizing gene gain/loss events as central to pathovar-specific metabolic and virulence traits. These findings identify novel molecular markers with potential applications in diagnostics and targeted disease control strategies. In particular, the characterization of conserved and lineage-specific effector repertoires provides a framework to inform strategies for breeding resistance through the identification of candidate targets for durable host immunity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circular RNA profiling uncovers regulators of early body color transition in juvenile leopard coral grouper (Plectropomus leopardus).","authors":"Xianwu Deng, Chenxian Huang, Qiuyan Wu, Silvana Rahayu, Xi Liu, Lei Pang, Fen Hu, Huapu Chen, Chunhua Zhu, Mouyan Jiang","doi":"10.1186/s12864-026-12896-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12896-4","url":null,"abstract":"<p><strong>Background: </strong>The leopard coral grouper is a valued aquaculture species whose market value is influenced by its body color. Current research on its coloration focuses on adults, leaving early developmental mechanisms unclear. Circular RNAs are important regulators in various processes, including pigmentation. This study aimed to explore the role of circRNAs in early color formation of leopard coral grouper.</p><p><strong>Results: </strong>Using skin tissues from transparent (26 dph) and newly pigmented red (30 dph) juveniles, we identified 42 differentially expressed circRNAs. Their source genes were enriched in pathways like Hedgehog signaling, cAMP signaling, and carotenoid metabolism. Four key circRNAs were identified, and a circRNA-miRNA network analysis suggested their involvement in melanin synthesis, pigment cell development, and carotenoid metabolism. The qPCR verification results were consistent with the trends in the sequencing results.</p><p><strong>Conclusions: </strong>This study provides the first circRNA profile during early color transition in leopard coral grouper, revealing a potential post-transcriptional regulatory network. The findings offer new insights into pigmentation mechanisms and provide valuable candidates for molecular-assisted breeding of color traits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association analysis reveals genetic variations and candidate genes associated with tannin and starch contents in sorghum.","authors":"Xinqi Fan, Du Liang, Chenchen Wang, Yizhong Zhang, Qi Guo, Huiyan Wang, Chunhong Li, Xinlian Shen, Qingshan Liu, Peng Xu","doi":"10.1186/s12864-026-12914-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12914-5","url":null,"abstract":"<p><strong>Background: </strong>Sorghum is the key grain for brewing distilled liquors. Grain composition, particularly tannin and starch levels, is closely linked to the sensory characteristics and yield of the final product. Developing elite sorghum cultivars with suitable tannin and elevated starch content is thus essential for producing liquors with diverse and distinct aroma profiles. Investigating the natural variations of grain composition in sorghum germplasms and identifying underlying genetic loci can facilitate the improvement of sorghum's nutritional value.</p><p><strong>Results: </strong>This study established near-infrared reflectance spectrometer (NIRS) non-destructive calibration models for determining sorghum tannin and starch contents based on phenotypic identification of 214 representative sorghum cultivars. A genome-wide association study (GWAS) of tannin and starch contents was performed based on two years and two locations of phenotypic data. A total of 18 associations with 338 single nucleotide polymorphisms (SNPs) scattered over 4 chromosomes were detected significantly associated with tannin and starch contents. Among these, two associations for tannin content and two associations for starch content were expressed in different environments, indicating that they were likely to be stable quantitative trait loci (QTLs). Through linkage disequilibrium (LD) block and haplotype analysis, a promising gene, Sobic.003G118266, which encodes chalcone synthase (CHS), was identified as orthologous to structural genes in known tannin synthesis pathways; while another promising gene, Sobic.004G353100, annotated as a glucose-6-phosphate translocator (G6PT), was determined to be a putative regulatory node in plant starch synthesis.</p><p><strong>Conclusion: </strong>These results provided important genetic variations and candidate genes to accelerate the improvement of sorghum breeding for liquor-brewing quality related traits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single cell RNA sequencing reveals transitional states and signaling shifts in nephron progenitor cells of the late-gestation rhesus macaque kidney.","authors":"Kairavee Thakkar, Sunitha Yarlagadda, Lyan Alkhudairy, Andrew Potter, Konrad Thorner, Praneet Chaturvedi, Cristina Cebrian, Kyle W McCracken, Nathan Salomonis, Raphael Kopan, Meredith P Schuh","doi":"10.1186/s12864-026-12908-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12908-3","url":null,"abstract":"<p><strong>Background: </strong>Human nephrogenesis is complete at 34-36 weeks gestation, with 60% of nephrons forming during the third trimester through lateral branch nephrogenesis (LBN). Currently, no mechanism exists for LBN as there are no late gestation human kidney transcriptional datasets. We hypothesized that an induced but dividing population of nephron progenitor cells (NPCs) would contribute to the amplification of nephrons in late gestation. We used the rhesus macaque, an established model of LBN, to help identify potential mechanisms.</p><p><strong>Methods: </strong>Single-cell RNA-sequencing (scRNA-Seq) was performed on cortically-enriched fetal rhesus kidneys (n = 9) from late second trimester and third trimester during LBN. This data was integrated with publicly available human scRNA-seq datasets from 8-18 weeks gestation kidneys (n = 8) using Harmony package. Differentially expressed genes and ligand-receptor interactions were assessed and validated using RNAScope™ on human and rhesus archival tissue.</p><p><strong>Results: </strong>Label transfer of previously defined kidney cell populations was performed on scRNA-seq data from 64,782 rhesus cells, including 7,879 nephron progenitor cells (NPCs) identified based on marker gene expression. Pseudotime analyses identified a late gestation-specific lineage branch of induced NPC in rhesus that was not observed in mid-gestation humans. Differential expression analyses identified increased SFRP1, FZD4, and TLE2 and decreased FZD7, SHISA2, SHISA3, and TLE4 within the late-gestation rhesus NPC compared to mid-gestation human NPC and increased SEMA3D within the rhesus ureteric bud (UB) tip, suggesting a compositional shift in WNT and SEMA signaling components within the naive NPC population during LBN.</p><p><strong>Conclusion: </strong>The rhesus macaque uniquely enables molecular studies of late-gestation primate nephrogenesis. Our study suggests the hypothesis that a transitional state of self-renewing NPCs supported by compositional shifts in key pathways may underlie the switch from branching phase nephrogenesis to lateral branch nephrogenesis and support ongoing nephron formation in late gestation. However, it remains to be determined if these changes within the late gestation NPC are time-dependent or species-dependent.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linking somatic mutations in cancer to the electronic properties of DNA.","authors":"Benoît de Witte, Cyril Karamaoun, Pauline Hermans, Maxime Tarabichi, Fabrizio Pucci, Marianne Rooman","doi":"10.1186/s12864-026-12879-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12879-5","url":null,"abstract":"<p><p>Oxidative stress, generated by both endogenous and exogenous agents, can cause DNA lesions that, if not repaired, accumulate as somatic mutations and can contribute to cancer initiation. Here, we explored this problem through the lens of DNA electronic properties, quantified by the vertical ionization potential (vIP) of nucleobase motifs, which reflects their susceptibility to oxidation. We analyzed genome-wide experimental data on oxidative DNA damage and found that the highest damage levels occur in regions with low vIP values, suggesting a causal link between them. The analysis of cancer mutational signatures and their annotated aetiologies revealed strong anticorrelations between mutation frequency and vIP values, particularly in cancers driven by oxidative DNA damage, such as lung cancer. We further computed anticorrelations between vIP values and the frequencies of mutated motifs across coding and non-coding regions and across different mutation types, observing the strongest anticorrelations for silent mutations, consistent with their reduced selective pressure. Moreover, similar anticorrelations were observed for somatic mutations in cancer and normal tissues, as well as for germline mutations, suggesting that they arise from similar mutagenesis processes. This work clarifies how oxidative damage, DNA electronic properties and carcinogenesis are related and help identify genomic regions more prone to mutations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).","authors":"Arno Hagenbeek, Yumiko Masukagami, Pradeep Palanichamy, Filip Husnik","doi":"10.1186/s12864-026-12881-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12881-x","url":null,"abstract":"<p><p>The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}