BMC Genomics最新文献

{"title":"Comparative genomics of nicotinic acetylcholine receptors reveals early divergence of the α6 subunit in cryptic Anopheles species.","authors":"Caroline Fouet, Desiree E Rios, Fred A Ashu, Matthew J Pinch, Cesar A Hernandez, Marilene M Ambadiang, Basile Kamgang, Colince Kamdem","doi":"10.1186/s12864-026-12994-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12994-3","url":null,"abstract":"<p><strong>Background: </strong>Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that mediate fast cholinergic transmission in the insect central nervous system and serve as targets for several widely used classes of insecticides. nAChR-targeting formulations are being deployed in malaria vector control programs to mitigate widespread resistance to pyrethroids. However, the extent of genetic variation at insecticide target sites that may facilitate evolutionary responses to chemical exposure among vector species remains poorly understood.</p><p><strong>Results: </strong>Here, we used whole-genome and Sanger sequencing to examine amino acid substitutions across all 11 nAChR subunits in sibling species of the Anopheles gambiae complex in Africa. The gene family is highly constrained, with only 33 nonsynonymous mutations detected at very low frequency in wild populations throughout the continent. No substitutions were observed at canonical ligand-binding residues within orthosteric domains, suggesting that acetylcholine and neonicotinoid binding affinities are unlikely to differ between the cryptic species. However, despite the evolutionary constraint, we identified two linked amino acid substitutions in the α6 subunit indicating early divergence of the receptor between species.</p><p><strong>Conclusions: </strong>These findings show that relaxed constraint can enable subtle amino acid changes in specific subunits of a conserved receptor family. The role of these mutations in shaping heterogeneous responses to insecticide exposure among mosquito species warrants further investigation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762396","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":"Transcriptomic sequencing reveals dynamic shifts in nutrient utilization and energy metabolism during embryonic and larval development of the purple sea urchin Heliocidaris crassispina.","authors":"Zepeng Zhang, Fanjiang Ou, Jianfeng Xu, Zhou Qin, Wenjie Pan, Yi Zhang, Youkai Tu, Jiasheng Huang, Yang Liu, Aifen Yan, Haipeng Qin, Chunhua Ren, Chaoqun Hu, Hongyan Sun, Xiao Jiang, Ting Chen","doi":"10.1186/s12864-026-13190-z","DOIUrl":"https://doi.org/10.1186/s12864-026-13190-z","url":null,"abstract":"<p><strong>Background: </strong>Heliocidaris crassispina is an economically important sea urchin in the Northwest Pacific, yet large-scale aquaculture is constrained by high mortality during early development. This limitation is largely attributable to the poor understanding of gene expression patterns across these critical stages. Therefore, a stage-resolved developmental transcriptomic profile from fertilization to the settled juvenile is needed to clarify the molecular basis of early developmental transitions and to support improved hatchery management and stage-appropriate feeding.</p><p><strong>Results: </strong>We described a complete developmental profile of H. crassispina from fertilization to the settled juvenile and established transcriptomes for 14 consecutive developmental stages. Beginning with the two-arm pluteus stage, H. crassispina undergoes rapid growth, paralleling a marked rise in mortality that continues through metamorphosis until the juvenile settles. Based on global gene expression patterns, development was divided into four periods. Period-I spanned the fertilized egg to 32-cell stages, Period-II covered two late-cleavage stages (LC1-LC2), Period-III extended from blastula to two-arm pluteus, and Period-IV extended from the four-arm pluteus to the settled juvenile stages. GO and KEGG analyses indicated a stepwise transition in gene expression programs across developmental periods, consistent with the morphological and physiological changes observed. Weighted gene co-expression network analysis (WGCNA) identified ten modules whose expression profiles correlated significantly with specific developmental periods, indicating development is regulated by a coordinated, module-level transcriptional program. Analysis of digestive enzyme and energy metabolism genes showed that early embryos rely on endogenous reserves, whereas feeding larvae progressively establish exogenous digestive capacity, accompanied by stage-dependent fluctuations and a late-stage rise in glycolysis and TCA cycle gene expression, suggesting a metabolic transition associated with exogenous feeding and settlement.</p><p><strong>Conclusion: </strong>This study established transcriptomes for 14 consecutive stages of H. crassispina from fertilization to the settled juvenile and, together with growth and survival, resolved four transcriptomic periods. Functional enrichment and WGCNA indicated coordinated, period-specific programs that track major morphological and physiological transitions. Digestive enzyme and energy metabolism genes showed a clear shift from reliance on endogenous reserves in embryos to the progressive establishment of exogenous digestive capacity in feeding larvae, accompanied by late-stage upregulation of glycolysis and TCA cycle genes around settlement. These insights support stage-specific feeding and hatchery management to reduce mortality.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262433","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":"The origin and evolution of tuna sex chromosomes.","authors":"Peter M Grewe, Jillian M Hammond, Andre L M Reis, Floriaan Devloo-Delva, Igor Stevanovski, Jorden Aulich, Nicola Potter, John R Hyde, Clare E Holleley, Adriane C Machado, Damian Jaccoud, Campbell R Davies, Ira W Deveson","doi":"10.1186/s12864-026-13229-1","DOIUrl":"https://doi.org/10.1186/s12864-026-13229-1","url":null,"abstract":"<p><p>Vertebrate species exhibit a variety of different systems for sex determination, with the most varied found among teleost fish. The genomic events through which new mechanisms are established are fundamental to our understanding of evolution. Here we describe a genomic rearrangement that gave rise to new sex chromosomes in tuna. We assembled highly complete genome sequences for all eight living true tuna species (genus Thunnus), skipjack tuna (Katsuwonus pelamis), and narrow-barred Spanish mackerel (Scomberomorus commerson) - a close relative of the tunas. We identified an inter-chromosomal translocated gene duplication, producing a single gene candidate controlling sex determination, SULT1-Y. This male-specific gene was shared among all tuna species, including skipjack. However, it was absent in Spanish mackerel, as well as more distantly related members of family Scombridae. We hypothesise that this genomic rearrangement, which appears to coincide with the origin of the Thunnus/Katsuwonus clade, conferred a new mode of genetic sex determination. In doing so, we speculate that it may have played a role in their speciation. Finally, we applied this new knowledge to develop SexXY'Plex, a DNA test for tuna sex assignment, providing an important new tool for tuna genetics research, fisheries management and conservation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262443","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":"Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny.","authors":"Yang Huang, Wenxiu Tang, Secai Huang, Chao Xiong, Lan Wu","doi":"10.1186/s12864-026-13066-2","DOIUrl":"https://doi.org/10.1186/s12864-026-13066-2","url":null,"abstract":"<p><strong>Background: </strong>Begonia, a hyperdiverse genus with ecological and medicinal values, confronts challenges in species identification and phylogenetic resolution due to remarkable morphological plasticity and ambiguous taxonomic boundaries. Chloroplast genomes (plastomes) serve as powerful molecular tools for addressing these issues, yet comprehensive plastomic data for Chinese Begonia species remain insufficient. This study presents the largest plastome dataset for Chinese Begonia (76 plastomes total), identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.</p><p><strong>Methods: </strong>We sequenced and assembled plastomes of 25 Chinese Begonia species, integrating 51 public plastomes for comparative analyses, including plastome structure, repeat dynamics, codon usage, nucleotide polymorphism, phylogenetics (ML/BI), and positive selection (Ka/Ks, BEB tests).</p><p><strong>Results: </strong>All 25 assembled plastomes exhibited a conserved quadripartite structures (167,365 - 169,901 bp) with 142-143 genes. Eleven hypervariable regions (e.g., ycf1, petB, ndhF-rpl32) were identified as potential DNA barcodes. Phylogenetic tree aligned with geographic distributions, clarifying taxonomic positions (e.g., B. mashanica). Five genes (matK, ndhB, ndhD, rps8, and rps15) showed candidate signals of positive selection, suggesting candidate loci for shade adaptation that require functional validation.</p><p><strong>Conclusion: </strong>This study enriches Begonia plastome resources, provides reliable molecular markers for species authentication, and sheds light on adaptive evolution. The findings support sustainable utilization of medicinal Begonia and advancing genus-level evolutionary and taxonomic research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262426","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":"Full-length transcriptome analysis reveals candidate genes involved in phenylpropanoid pathway in Euphorbia maculata.","authors":"Sanbao Guo, Meiling Song, Mingming Gui, Wuhua Yu, Qingyang Wu, Zechang Rao, Zirun Zhang, Chunxiang Chen, Shenghe Huang","doi":"10.1186/s12864-026-13213-9","DOIUrl":"https://doi.org/10.1186/s12864-026-13213-9","url":null,"abstract":"<p><strong>Background: </strong>Euphorbia maculata is a herbaceous plant in China, known for its medicinal properties. The main active components of E. maculata are flavonoids. However, the biosynthesis mechanism of flavonoids in E. maculata remains poorly understood due to the limited availability of genetic information. In order to explore the flavonoid biosynthesis mechanism of this species, we carried our study.</p><p><strong>Results: </strong>A total of 20,238 non-redundant transcript isoforms were acquired with an N50 length of 2,994 bp and an average length of 2,766.82 bp. Of these isoforms, 20,069 (99.16%) were successfully annotated in NR, Swissprot, KOG, GO, and KEGG databases. Additionally, 20,085 coding sequences (CDSs), 117 long noncoding RNAs (LncRNAs), and 971 transcription factors (TFs) were identified from the full-length transcriptome data. The RNA-Seq data was then analyzed using the full-length transcriptome as a reference sequence, revealing 27 differentially expressed genes (DEGs) involved in phenylpropanoid pathway in E. maculata. These included 15 PAL, 5 C4H, 4 4CL, and 3 CHS genes. The expression levels of these DEGs were found to vary in the leaf and stem across five different periods, with the majority of phenylpropanoid pathway genes being upregulated in the stem compared to the leaf at the same period. Protein-protein interaction (PPI) analysis revealed that the bHLH, HD-ZIP, bZIP, MYB, FAR1, and AP2 may regulate the expression of 5 C4H and 3 CHS. Furthermore, through analyzing the correlation between the expression levels of DEGs and the accumulation of flavonoids in various tissues of E. maculata at different stages, we found that 2 PAL, 2 C4H, 1 4CL, and 2 CHS may play a crucial role in regulating flavonoid biosynthesis in this species.</p><p><strong>Conclusions: </strong>Our study enriched the genomic resources and revealed candidate genes involved in phenylpropanoid pathway in E. maculata. These findings provide candidate gene resources for further investigation of the flavonoid biosynthesis mechanism in E. maculata.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262370","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":"DynML-Net: a porcine enteric virus identification network based on protein language models and a dynamic heterogeneous multi-branch architecture.","authors":"Qingwei Chen, Xin Xing, Shumei Li, Ying Shao, Xiangjun Song, Zhao Qi","doi":"10.1186/s12864-026-13227-3","DOIUrl":"https://doi.org/10.1186/s12864-026-13227-3","url":null,"abstract":"<p><strong>Background: </strong>Porcine Enteric Viruses (PEVs) pose a serious threat to the global pig industry, leading to substantial economic losses. However, traditional clinical diagnostic methods are limited by high costs, long turnaround times, and difficulties in rapidly addressing challenges such as co-infections with multiple viruses and the emergence of different viral species. To overcome the limitations of existing approaches in recognizing viruses under complex clinical conditions, poor adaptability to variant strains, and the insufficient extraction of key features, this study proposes a deep learning network integrating the ESM-2 protein language model and a multi-branch heterogeneous architecture, named DynML-Net.</p><p><strong>Results: </strong>The model adaptively integrates decision outputs representing local architectural patterns, global dependencies, and long-sequence evolutionary features through a dynamic gating mechanism, and enhances classification performance via a deep mutual learning (DML) strategy. Experimental results demonstrate that DynML-Net achieves accuracies of 94.52% and 89.16% for binary and multiclass classification tasks, respectively, outperforming current mainstream models, while exhibiting robust performance under conditions of sample imbalance, data reduction, and heterologous viral datasets scenarios.</p><p><strong>Conclusions: </strong>This study demonstrated the efficacy of DynML-Net in PEVs identification and classification tasks, and based on DynML-Net, a Streamlit-based locally deployable system was developed to facilitate a closed-loop workflow from sequence upload to automated identification, providing an accurate and efficient computational solution for the rapid detection of PEVs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149242886","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":"A highly contiguous de novo genome assembly of the Mexican Duck (Anas diazi) reveals fine-scale structural variation within the mallard complex.","authors":"Patricia Padilla-Aguilar, María Guadalupe Bravo-Vinaja, Edmundo Gutiérrez-Morales, David Colón-Quezada, Gastón Contreras-Jiménez, Marco Tulio Solano-De la Cruz","doi":"10.1186/s12864-026-13219-3","DOIUrl":"https://doi.org/10.1186/s12864-026-13219-3","url":null,"abstract":"<p><p>The Mexican Duck (Anas diazi) is a quasi-endemic North American dabbling duck whose evolutionary history is marked by recent Pleistocene divergence and ongoing introgressive hybridization with the Mallard (Anas platyrhynchos). Because the two species are morphologically and genomically very similar, identifying where their genomes differ structurally is central to understanding how species integrity is maintained under gene flow. Here we present the first highly contiguous de novo genome assembly of A. diazi (PacBio HiFi) and use it to map chromosomal inversions across the phylogeny of the mallard complex. k-mer profiling revealed high heterozygosity (1.08%), and read-depth haplotype purging recovered an accurate 1.19 Gb haploid consensus (BUSCO 95.7%). Using independent, orientation-aware approaches-including read-based structural-variant detection and phylogenetic polarization-we find that structural differences between A. diazi and the Mallard are numerous but small (kb-scale), and strongly enriched on the Z chromosome. Loci within these species-specific inversions (e.g., PIK3C3, RIT2, and DIPK2B) exhibit high structural protein conservation, while functional annotation highlights post-transcriptional mechanisms. Furthermore, the capture of master non-coding RNAs within these rearrangements, including the spliceosomal U1 and the nucleolar SNORA5, provides a mechanism for species-specific alternative splicing and translational control. Ultimately, we find no evidence for macro-inversion 'supergenes'; instead, the Mexican Duck maintains its divergence through fine-scale, Z-concentrated and post-transcriptional rewiring, consistent with the genomic architecture of recently diverged, hybridizing lineages.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149242944","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":"Unraveling the genetic underpinnings of fat metabolism and SDR16C5 mediated molecular mechanisms in adipogenesis of domestic pigs.","authors":"Pengtao Yuan, Peng Su, Rundong Ma, Yitian Ma, Yuehui Ma, Lin Jiang, Dandan Wang","doi":"10.1186/s12864-026-13159-y","DOIUrl":"https://doi.org/10.1186/s12864-026-13159-y","url":null,"abstract":"<p><strong>Background: </strong>Fat metabolism plays a pivotal role in determining meat quality and economic value in domestic pigs, yet its underlying genetic mechanisms remain poorly understood. To clarify the molecular basis of adipose deposition, this study integrated whole-genome resequencing data from 226 individuals across 61 Eurasian pig breeds and applied population genetic and selective sweep analyses to identify and validate candidate genes involved in fat metabolism.</p><p><strong>Results: </strong>Significant genetic divergence was observed between Asian and European domestic pigs, with higher linkage disequilibrium (LD) levels in domestic breeds likely driven by artificial selection during domestication. High-fat groups (backfat thickness: 39 mm; fat percentage: 35%) exhibited substantially greater fat deposition than low-fat groups (backfat thickness: 15 mm; fat percentage: 15%). Combined analyses of Pi-ratio, XP-EHH, and F_ST revealed 13 key candidate genes, including SDR16C5 and CPE, functionally enriched for lipid metabolism pathways such as fatty acid metabolism and insulin signaling. Cellular assays further confirmed that SDR16C5 promotes adipogenesis by enhancing preadipocyte proliferation and lipid accumulation.</p><p><strong>Conclusion: </strong>This study identifies SDR16C5 as a candidate regulator of adipogenesis and fat metabolism in pigs. These findings establish a genetic framework that may facilitate targeted breeding strategies to improve fat composition and enhance premium pork production.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149262449","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":"SFOA-based optimized SeResNet-BiLSTM network with an attention mechanism for the detection of exons.","authors":"Jayasree K, Malaya Kumar Hota","doi":"10.1186/s12864-026-13194-9","DOIUrl":"10.1186/s12864-026-13194-9","url":null,"abstract":"<p><p>Detection of exons in eukaryotic DNA sequences is a challenging research area in computational biology. In this work, a Starfish Optimization Algorithm (SFOA) based hybrid deep learning architecture is proposed for the efficient detection of exons, which is the amalgamation of squeeze and excitation residual network (SeResNet), bidirectional long short-term memory (BiLSTM), and a customized attention (CA) mechanism. Firstly, SeResNet retrieves the deeply hidden features by performing recalibration and interdependencies between the channels. After that, BiLSTM is utilized to extract temporal information for a better understanding of the input data. Later, a CA mechanism is employed to select the salient features by redistributing the feature weights obtained from the SeResNet-BiLSTM to enhance the detection accuracy. Finally, the SFOA is applied to automatically optimize the hyperparameters of the SeResNet-BiLSTM-CA framework to improve the feature extraction. Before applying the deep learning framework, the modified Gabor wavelet transform (MGWT) is used to extract the periodic feature information. The efficacy of the proposed model is validated using two benchmark datasets, namely the HMR195 and the Genscan training set. To verify the efficiency of the proposed method, its performance is compared with several pre-trained networks and various existing techniques using evaluation metrics. The simulation outcomes confirmed that the proposed SFOA-based hybrid optimized SeResNet-BiLSTM-CA model achieves superior performance than its counterparts.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13689209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149236824","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":"Histology images in spatial transcriptomics: a critical evaluation of their effectiveness in spatial domain detection.","authors":"Abdullah Al Noman, Asif Ajrof, Md Abul Hassan Samee, M Saifur Rahman","doi":"10.1186/s12864-026-12830-8","DOIUrl":"10.1186/s12864-026-12830-8","url":null,"abstract":"<p><strong>Motivation: </strong>Spatial transcriptomics (ST) has become a powerful tool for studying gene expression at the spatial level, as the position of a given spot provides crucial information about its phenotype. One key application of downstream analysis on these ST datasets is identifying spatial domains within tissue regions. However, the accuracy of spatial domain detection can be hindered by technical noise and low resolution due to technological limitations. Some ST technologies now provide high-resolution histology images of the original tissue sample prior to sequencing, offering complementary information. Incorporating these histology images presents a promising approach to addressing these limitations. However, there is a scarcity of reviews on recent methods that use histology images for spatial domain detection tasks. Also, it remains unclear how much improvement is gained by these methods when integrating histology image with ST data over using ST data alone.</p><p><strong>Results: </strong>This article presents an analysis of various methodologies that integrate histology images for spatial domain detection. We describe the specific challenges these methods address in incorporating histology images alongside gene expression data, highlighting both their commonalities and distinctions. Furthermore, we design a statistical test to systematically determine the significance of domain quality improvement with the additional modality of histology images, if any, by comparing the performance of methods run both with and without the histology data. Furthermore, we conduct statistical tests to determine the significance of histology images in improving spatial domain detection tasks. Our findings indicate no notable enhancement in spatial domain detection when histology images are used as an additional source of information alongside gene expression data for the methods under study. Building on these results, we investigate the possible reasons why histology images may fail to improve performance and discuss future directions for their effective integration in spatial domain detection.</p><p><strong>Availability and implementation: </strong>Source code is available at Github ( https://github.com/asifajrof/StHistDDComp ).</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13688954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149236855","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}