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Localization of the origin of transfer for Salmonella genomic island 4 from Salmonella enterica serovar I 4,[5],12:i:. 肠炎沙门氏菌基因组岛4 （SGI-4）转移源定位[j] .浙江大学学报（自然科学版），2010,12:1 - 8。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf023

Durga P Neupane, Bradley L Bearson, Shawn M D Bearson

{"title":"Localization of the origin of transfer for Salmonella genomic island 4 from Salmonella enterica serovar I 4,[5],12:i:.","authors":"Durga P Neupane, Bradley L Bearson, Shawn M D Bearson","doi":"10.1093/dnares/dsaf023","DOIUrl":"10.1093/dnares/dsaf023","url":null,"abstract":"Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) is one of the most frequent multidrug-resistant (MDR) Salmonella serovars associated with food-animal production globally, and strains often contain Salmonella genomic island-4 (SGI-4), an integrative conjugative element (ICE) encoding metal tolerance for copper, silver, and arsenic. Horizontal gene transfer (HGT) of SGI-4 from serovar I 4,[5],12:i:- to recipient bacteria results in enhanced metal tolerance for the transconjugants; however, the origin of transfer (oriT) for SGI-4 mobilization is unknown. In this study, the oriT within SGI-4 of MDR serovar I 4,[5],12:i:- strain USDA15WA-1 was identified by (i) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and (ii) deleting the predicted oriT region of SGI-4 from strain USDA15WA-1 and abolishing SGI-4 transfer. Sequence similarity to oriTSGI-4 was identified in other Enterobacteriaceae, and conjugation of SGI-4 occurred from USDA15WA-1 to Salmonella serovars from Serogroups C-E as well as Escherichia coli and Citrobacter. Localization of the SGI-4 oriT enhances our understanding of a DNA region involved in HGT of an ICE in a frequent MDR Salmonella serovar, thereby providing a model to investigate HGT of SGI-4 and dissemination of metal tolerance genes in the food-animal production environment.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12969280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092718","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}

引用次数: 0

Nuclear genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis. 核基因组测序揭示了chlorarachniophyte藻类Amorphochlora amoebiformis的高度内含子丰富的结构。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf035

Daichi Aoki, Honoka Saiki, Kenta Yamamoto, Shigekatsu Suzuki, Yoshihisa Hirakawa

{"title":"Nuclear genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis.","authors":"Daichi Aoki, Honoka Saiki, Kenta Yamamoto, Shigekatsu Suzuki, Yoshihisa Hirakawa","doi":"10.1093/dnares/dsaf035","DOIUrl":"10.1093/dnares/dsaf035","url":null,"abstract":"Chlorarachniophyte algae possess complex plastids derived from endosymbiosis between a cercozoan protist and green alga. As evidence of this event, remnant nucleus of the endosymbiont, nucleomorph, is present in the plastid intermembrane space. Chlorarachniophytes are excellent models to study genome evolution via endosymbiosis. Although the three organelle genomes of mitochondrion, plastid, and nucleomorph have been sequenced in several chlorarachniophyte species, nuclear genome information is currently limited to Bigelowiella natans. To gain insights into the genome diversity and evolution of chlorarachniophytes, we sequenced the nuclear genome of another chlorarachniophyte, Amorphochlora amoebiformis. Its size is approximately 214 Mb, which is more than twice that of B. natans. Remarkably, three-quarters of the nuclear genome encodes spliceosomal introns, indicating its highly intron-rich structure compared to other known eukaryotic genomes. Single nucleotide polymorphism analysis revealed that A. amoebiformis possessed a diploid nuclear genome, unlike the haploid genome of B. natans. Additionally, we identified organellar DNA fragments within the nuclear genome, suggesting recent DNA migration from the three organelles to the nucleus. Overall, our findings reveal that chlorarachniophyte nuclear genomes differ substantially in size, structure, and ploidy across species, and provide evidence of ongoing endosymbiotic gene transfer.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12730881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145642396","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}

引用次数: 0

Full-length hybrid transcriptome of the olfactory rosette in Senegalese sole (Solea senegalensis): an essential genomic resource for improving reproduction on farms. 塞内加尔鳎（Solea senegalensis）嗅觉莲座的全长杂交转录组：改善农场繁殖的重要基因组资源。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf028

Dorinda Torres-Sabino, Andrés Blanco-Hortas, Paula R Villamayor, Inmaculada Rasines, Ignacio Martín, Carmen Bouza, Diego Robledo, Paulino Martínez

{"title":"Full-length hybrid transcriptome of the olfactory rosette in Senegalese sole (Solea senegalensis): an essential genomic resource for improving reproduction on farms.","authors":"Dorinda Torres-Sabino, Andrés Blanco-Hortas, Paula R Villamayor, Inmaculada Rasines, Ignacio Martín, Carmen Bouza, Diego Robledo, Paulino Martínez","doi":"10.1093/dnares/dsaf028","DOIUrl":"10.1093/dnares/dsaf028","url":null,"abstract":"Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made recently, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing. A total of 20,670 transcripts actively expressed were identified: 13,941 known transcripts, 5,758 novel transcripts from known genes, and 971 from novel genes. Given the important role of olfaction in reproductive behaviour, we comparatively examined the expression and functional enrichment of the olfactory receptor gene families (OlfC, OR, ORA, and TAAR). Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12666390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240292","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}

引用次数: 0

Life inside a bag: multiomics insights into the bagworm species Eumeta crameri. 袋子里的生活：对袋虫物种真丝虫的多组学见解。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf029

Abhisek Chakraborty, Shruti Mahajan, Vishnu Prasoodanan P K, Akhilesh Shailendra Khamkar, Vineet K Sharma

{"title":"Life inside a bag: multiomics insights into the bagworm species Eumeta crameri.","authors":"Abhisek Chakraborty, Shruti Mahajan, Vishnu Prasoodanan P K, Akhilesh Shailendra Khamkar, Vineet K Sharma","doi":"10.1093/dnares/dsaf029","DOIUrl":"10.1093/dnares/dsaf029","url":null,"abstract":"Bagworms are commonly known for the well-organized case or bag surrounding them constructed using their silk and plant materials. To understand the genetic basis of these unique characteristics in bagworms, we performed multiomics analyses of a bagworm species, Eumeta crameri. The genome and transcriptome sequencing of E. crameri were used to construct the nuclear genome with a size of 668.2 Mb, N50 value of 6.6 Mb, and 13,554 coding genes, which was further assembled into 31 pseudochromosomes. The mitochondrial genome had a size of 15.6 Kb. We established the phylogenetic position of E. crameri with respect to 54 other insect species. The comparative analyses of E. crameri with other Lepidopterans revealed the adaptive evolution of genes related to primary metabolic pathways, defense, molting, and metamorphosis, and silk formation in the bagworm species. We also showed the ultrafine nature of the E. crameri silk fibres. Further, we performed the gut microbiome sequencing for E. crameri and constructed a gut microbial gene catalogue, which revealed the unique composition of the gut microbiome and its significance for host metabolism and defense. Together, the results provide multifaceted insights into the biological processes that support the well-organized holometabolous metamorphosis inside the bags of E. crameri.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12666389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356486","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}

引用次数: 0

Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases. 迈向包含甲基化碱基的扩展核苷酸密码的分子进化表观基因组学。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf025

Shinya Yoshida, Ikuo Uchiyama, Masaki Fukuyo, Mototsugu Kato, Desirazu N Rao, Mutsuko Konno, Shin-Ichi Fujiwara, Takeshi Azuma, Ichizo Kobayashi, Hirohisa Kishino

{"title":"Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.","authors":"Shinya Yoshida, Ikuo Uchiyama, Masaki Fukuyo, Mototsugu Kato, Desirazu N Rao, Mutsuko Konno, Shin-Ichi Fujiwara, Takeshi Azuma, Ichizo Kobayashi, Hirohisa Kishino","doi":"10.1093/dnares/dsaf025","DOIUrl":"10.1093/dnares/dsaf025","url":null,"abstract":"In molecular evolution analyses, genomic DNA sequence information is usually represented in the form of 4 bases (ATGC). However, research since the turn of the century has revealed the importance of epigenetic genome modifications, such as DNA base methylation, which can now be decoded using advanced sequence technologies. Here we provide an integrated framework for analyzing molecular evolution of nucleotide substitution, methylation, and demethylation using an expanded nucleotide code that incorporates different types of methylated bases. As a first attempt, we analysed substitution rates between bases, both unmethylated and methylated ones. As the model methylomes, we chose those of Helicobacter pylori, a unicellular bacterium with the largest known repertoire of sequence-specific DNA methyltransferases. We found that the demethylation rates are remarkably high while the methylation rates are comparable with the substitution rates between unmethylated bases. We found that the ribosomal proteins known for sequence conservation showed high methylation and demethylation frequencies, whereas the genes for DNA methyltransferases themselves showed low methylation and demethylation frequencies compared to base substitution. This study represents the first step toward molecular evolutionary epigenomics, which, we expect, would contribute to understanding epigenome evolution.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12666383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092730","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}

引用次数: 0

Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus. 两种野生开花樱桃（itosakura Cerasus和C. jamasakura）的染色体规模基因组为樱花的结构进化提供了见解。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf031

Kazumichi Fujiwara, Atsushi Toyoda, Toshio Katsuki, Yutaka Sato, Bhim B Biswa, Takushi Kishida, Momi Tsuruta, Yasukazu Nakamura, Takako Mochizuki, Noriko Kimura, Shoko Kawamoto, Tazro Ohta, Ken-Ichi Nonomura, Hironori Niki, Hiroyuki Yano, Kinji Umehara, Chikahiko Suzuki, Tsuyoshi Koide

{"title":"Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus.","authors":"Kazumichi Fujiwara, Atsushi Toyoda, Toshio Katsuki, Yutaka Sato, Bhim B Biswa, Takushi Kishida, Momi Tsuruta, Yasukazu Nakamura, Takako Mochizuki, Noriko Kimura, Shoko Kawamoto, Tazro Ohta, Ken-Ichi Nonomura, Hironori Niki, Hiroyuki Yano, Kinji Umehara, Chikahiko Suzuki, Tsuyoshi Koide","doi":"10.1093/dnares/dsaf031","DOIUrl":"10.1093/dnares/dsaf031","url":null,"abstract":"Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. ×yedoensis \"Somei-yoshino,\" and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of \"Somei-yoshino.\" Comparison with the phased genome of \"Somei-yoshino\" revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12666387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145402721","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}

引用次数: 0

Genome assembly and insights into globally invasive Red-vented Bulbul (Pycnonotus cafer). 基因组组装和对全球入侵红气孔球（Pycnonotus cafer）的认识。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf027

Martin Abraham Puthumana, Manohar S Bisht, Mitali Singh, Vineet K Sharma

引用次数: 0

Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics. 利用单细胞基因组学和宏基因组学对复杂根际和土壤细菌群落进行菌株水平解剖。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf032

Masako Kifushi, Yohei Nishikawa, Masahito Hosokawa, Toyoaki Anai, Haruko Takeyama

{"title":"Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.","authors":"Masako Kifushi, Yohei Nishikawa, Masahito Hosokawa, Toyoaki Anai, Haruko Takeyama","doi":"10.1093/dnares/dsaf032","DOIUrl":"10.1093/dnares/dsaf032","url":null,"abstract":"Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12666376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145476835","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}

引用次数: 0

Whole-genome sequencing of wild and ancestral Dura provides insight into the untapped genomic information of undomesticated oil palm (Elaeis guineensis Jacq.). 野生和祖先硬脑膜的全基因组测序为未驯化油棕（Elaeis guineensis Jacq.）未开发的基因组信息提供了见解。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf033

Redi Aditama, Heri Adriwan Siregar, Zulfikar Achmad Tanjung, Diny Dinarti, Sintho Wahyuning Ardie, Willy Bayuardi Suwarno, Edy Suprianto, Condro Utomo, Tony Liwang, Sudarsono Sudarsono

{"title":"Whole-genome sequencing of wild and ancestral Dura provides insight into the untapped genomic information of undomesticated oil palm (Elaeis guineensis Jacq.).","authors":"Redi Aditama, Heri Adriwan Siregar, Zulfikar Achmad Tanjung, Diny Dinarti, Sintho Wahyuning Ardie, Willy Bayuardi Suwarno, Edy Suprianto, Condro Utomo, Tony Liwang, Sudarsono Sudarsono","doi":"10.1093/dnares/dsaf033","DOIUrl":"10.1093/dnares/dsaf033","url":null,"abstract":"Oil palm (Elaeis guineensis Jacq.) is a globally important crop, and its genetic improvements benefit from comprehensive genome sequencing. Here, we report the whole-genome sequencing and annotation of two key genetic resources: the wild (Eg-DCM) and ancestral (Eg-DBG) Dura accessions, using a combination of short- and long-read sequencing technologies. De novo assembly followed by polishing, proximity ligation, and reference-guided scaffolding yielded high-quality assemblies with ungapped lengths of 1.71 Gb (Eg-DBG) and 1.48 Gb (Eg-DCM). Eg-DCM and Eg-DBG genomes exhibited high completeness, with over 97% of Benchmarking Universal Single-Copy Orthologs (BUSCOs) recovered across the Eukaryota, Viridiplantae, and Embryophyta datasets. Repetitive elements, particularly retrotransposons, dominated both genomes, accounting for 46.10% of Eg-DBG and 43.85% of Eg-DCM. Gene prediction initially identified 61,256 (Eg-DBG) and 53,985 (Eg-DCM) genes, which were refined into high-confidence gene sets of 39,263 and 35,298, respectively. Additionally, 1,760 and 1,684 putative resistance (R) genes were identified in Eg-DCM and Eg-DBG, with similar class distributions. The five major R gene classes comprise KIN, RLK, RLP, CNL, and CK. With further research, the assembled whole-genome sequences and the annotated genes of Eg-DBG and Eg-DCM offer valuable insights into the untapped genomic information of undomesticated accessions, with implications for future breeding and crop improvement efforts of oil palm.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12730872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145565491","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}

引用次数: 0

Can classical statistics and deep learning converge on explainable, causally driven target discovery? 经典统计学和深度学习能在可解释的、因果驱动的目标发现上融合吗？

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf024

Liyin Chen

{"title":"Can classical statistics and deep learning converge on explainable, causally driven target discovery?","authors":"Liyin Chen","doi":"10.1093/dnares/dsaf024","DOIUrl":"10.1093/dnares/dsaf024","url":null,"abstract":"Understanding the molecular causes of complex diseases remains one of the most pressing challenges in biomedicine. Despite large-scale genome-wide association studies mapping thousands of risk loci, identifying which genetic variants truly drive disease remains difficult. Traditional statistical genetics has laid a strong foundation for variant discovery, but it often struggles to capture nonlinear interactions and cannot fully integrate the breadth of the interconnected multi-omics data. In recent years, deep learning approaches have shown promise in bridging these gaps: modelling high-order genetic interactions, uncovering latent biological structure, and enabling multi-layered data integration. However, most current deep learning models for genomics remain exploratory in nature, and issues such as susceptibility to overfitting, difficulties in interpretability, and the general lack of standardized evaluation frameworks have limited their widespread adoption for genomics research. In this review, we explore how traditional statistical and deep learning methods can be applied to uncover causal mechanisms in complex disease. We critically compare these two frameworks for their advantages and limitations in detecting genetic associations and prioritizing causal associations. Towards the end, we propose a future direction centred around hybrid models that blend the scalability of deep learning with the inferential power of statistical genetics. Our goal is to guide researchers in developing next-generation computational tools to uncover the molecular basis of complex diseases and accelerate the translation of genetic findings into effective treatments.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12628793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092784","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}

引用次数: 0