DNA Research最新文献

Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans. 银嵌合体基因组揭示了全头动物谱系特异性性染色体和视蛋白基因的进化。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-03-03 DOI: 10.1093/dnares/dsag003

Akinori Teramura, Mitsutaka Kadota, Shotaro Hirase, Shigehiro Kuraku, Kiyoshi Kikuchi

{"title":"Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.","authors":"Akinori Teramura, Mitsutaka Kadota, Shotaro Hirase, Shigehiro Kuraku, Kiyoshi Kikuchi","doi":"10.1093/dnares/dsag003","DOIUrl":"10.1093/dnares/dsag003","url":null,"abstract":"Cartilaginous fishes are divided into holocephalans and elasmobranchs, and they offer valuable systems for analysing the genetic basis of adaptation to diverse habitats and the evolution of chromosomal organization. Genomic studies on cartilaginous fishes were initiated early with holocephalans because of their compact genomes, but have concentrated primarily on the family Callorhinchidae. Here, we focused on the most species-rich holocephalan family Chimaeridae and characterized the genome of its member, silver chimaera (Chimaera phantasma), in pursuit of genomic traces of adaptation to deep-sea vision. The resulting genome assembly exhibited high continuity and completeness, enabling the first chromosome-level comparison among holocephalans. They displayed substantial intragenomic variation in chromosome length, correlated with intron size, alongside a high degree of one-to-one chromosomal homology. Our search for silver chimaera photoreceptor genes revealed a shrunken set of opsin genes, including rhodopsin exhibiting a sequence signature typical of deep-sea adaptation. We also performed whole-genome resequencing of multiple silver chimaera individuals of both sexes, which identified a putative X-chromosome fragment. This is the first evidence of a holocephalan sex chromosome and suggests male heterogametic sex determination. Our findings contribute to a deeper understanding of vertebrate genome diversity and lay the groundwork for future genetic studies on this species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12952989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146183380","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

AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars. AlleleMiner：一个长读管道，用于二倍体柑橘品种的基因新生等位基因相位和变异检测。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-03-03 DOI: 10.1093/dnares/dsag004

Yukinari Kiryu, Yoshihiro Kawahara, Tomoko Endo, Tokumasa Horiike, Kenta Shirasawa, Sachiko Isobe, Takehiko Shimada, Hiroshi Fujii

{"title":"AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars.","authors":"Yukinari Kiryu, Yoshihiro Kawahara, Tomoko Endo, Tokumasa Horiike, Kenta Shirasawa, Sachiko Isobe, Takehiko Shimada, Hiroshi Fujii","doi":"10.1093/dnares/dsag004","DOIUrl":"10.1093/dnares/dsag004","url":null,"abstract":"Allelic variation is a critical determinant of agronomic traits in heterozygous crops. Most existing approaches define variation as reference-anchored differences, such as SNPs or structural variants, confining allelic diversity to variant feature coordinates. Here, we present AlleleMiner, a Python-based pipeline that phases diploid gene sequences directly from PacBio HiFi reads. Rather than relying on reference-based coordinate systems for allele representation, AlleleMiner uses the reference genome solely to identify target gene region sequences and performs de novo assembly of read sets at each locus, minimizing reference dependence and reconstructing phased allele sequences. Across 18 citrus cultivars, the pipeline achieved an average phasing output of 91.5% of 1,409 single-copy genes, with coverage achieving. Coverage analyses using both real and simulated datasets indicated that a ∼30× HiFi depth is preferable for the stable recovery of heterozygous alleles, reducing potential allele dropout. Validation using pedigree information showed allele transmission patterns with known relationships. Using simulated haplotype data and the Citrus clementina assembly v1.0, AlleleMiner achieved complete-match reconstruction for both alleles at approximately 70% of loci. By enabling reference-minimized gene-level allele discovery, AlleleMiner provides a scalable framework for constructing allele databases and advancing marker-assisted and genomic selection in complex crops.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13011809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147345710","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

The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms. pleurossigma的基因组提供了对远洋硅藻进化适应的见解。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsaf037

Jianbo Jian, Chunhai Chen, Xiaodong Fang, Christopher T Workman, Thomas Ostenfeld Larsen, Yuhang Li, Eva C Sonnenschein

{"title":"The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms.","authors":"Jianbo Jian, Chunhai Chen, Xiaodong Fang, Christopher T Workman, Thomas Ostenfeld Larsen, Yuhang Li, Eva C Sonnenschein","doi":"10.1093/dnares/dsaf037","DOIUrl":"10.1093/dnares/dsaf037","url":null,"abstract":"The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins might facilitate the adaptation of P. pacificum to high-light conditions in pelagic environments. The percentage of approximately 3.2% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12803021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745639","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

Giant linear plasmids in Mycobacterium avium harbour a tRNA array unit. 鸟分枝杆菌巨型线性质粒中含有tRNA阵列单元。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsaf039

Hirokazu Yano, Kentaro Arikawa, Haruo Ikeda, Shouta Nonoyama, Fumito Maruyama, Seigo Kitada, Hiroshi Kida, Manabu Ato, Tomotada Iwamoto, Yukiko Nishiuchi

{"title":"Giant linear plasmids in Mycobacterium avium harbour a tRNA array unit.","authors":"Hirokazu Yano, Kentaro Arikawa, Haruo Ikeda, Shouta Nonoyama, Fumito Maruyama, Seigo Kitada, Hiroshi Kida, Manabu Ato, Tomotada Iwamoto, Yukiko Nishiuchi","doi":"10.1093/dnares/dsaf039","DOIUrl":"10.1093/dnares/dsaf039","url":null,"abstract":"Nontuberculous mycobacteria occasionally harbour clustered tRNA genes, referred to as a tRNA array unit, which is considered a putative antidefense system within their genomes. However, the precise genomic location of these tRNA array units remains unclear. To address this, we sequenced the complete genomes of 5 Mycobacterium avium strains carrying a tRNA array unit using a hybrid assembly of long and short reads followed by manual curation. The assemblies indicated that each strain harbours 3 to 5 extrachromosomal elements. In all genomes, the tRNA array unit was found on a linear contig exceeding 300 kb. Pulse-field gel electrophoresis (PFGE) and sodium dodecyl sulphate-PFGE revealed that the strains harbour linear plasmids corresponding to these large contigs with protein-capped termini. These linear plasmids encode a hybrid type VII/type IV secretion system but lack relaxase genes, which are typically present in mycobacterial circular plasmids. Additionally, they contain approximately 415 bp inverted repeats at the termini. Sequences of related plasmids were identified exclusively in the genomes of M. avium isolates from Japan available in public databases, suggesting a possible Asian origin. This study provides the first experimental evidence that M. avium harbours giant invertron-type linear plasmids carrying a tRNA array unit.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12803027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145893389","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-level genome assembly of the Gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies. 利用HiFi长读和Hi-C技术组装非洲菊（Gerbera hybrida）染色体水平基因组。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsag002

Yuta B Aoyagi, Riki Shimada, Hideki Hirakawa, Atsushi Toyoda, Hidehiro Toh, Sachiko Isobe, Naoyuki Tajima, Kenta Shirasawa, Tokumasa Horiike, Hiroshi Fujii, Tao Fujiwara, Masaru Bamba, Takashi Nakatsuka, Akiyoshi Tominaga

{"title":"Chromosome-level genome assembly of the Gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies.","authors":"Yuta B Aoyagi, Riki Shimada, Hideki Hirakawa, Atsushi Toyoda, Hidehiro Toh, Sachiko Isobe, Naoyuki Tajima, Kenta Shirasawa, Tokumasa Horiike, Hiroshi Fujii, Tao Fujiwara, Masaru Bamba, Takashi Nakatsuka, Akiyoshi Tominaga","doi":"10.1093/dnares/dsag002","DOIUrl":"10.1093/dnares/dsag002","url":null,"abstract":"Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of 2 wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. A syntenic analysis of the G. hybrida genome and published Asterales genomes demonstrated that Gerbera has undergone a whole-genome triplication. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12916149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121009","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

The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity. 中药牛的染色体水平基因组为牛的适应和免疫提供了新的思路。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsaf034

Fei Ge, Yingwei Guo, Lei Xu, Wai Yee Low, Haoran Ma, Qian Li, Zezhao Wang, Bo Zhu, Lingyang Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li, Yan Chen

{"title":"The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.","authors":"Fei Ge, Yingwei Guo, Lei Xu, Wai Yee Low, Haoran Ma, Qian Li, Zezhao Wang, Bo Zhu, Lingyang Xu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li, Yan Chen","doi":"10.1093/dnares/dsaf034","DOIUrl":"10.1093/dnares/dsaf034","url":null,"abstract":"Genomic research is currently undergoing a paradigm shift from reliance on a single reference sequence to the use of breed-specific genomes. Chinese indicine cattle (Bos taurus indicus), characterized by their notable tick resistance and heat tolerance, display extensively genetic diversity than taurine. Here, we generated a chromosome level genome assembly of Chinese indicine cattle, achieving a contiguity N50 of 90.92 Mb and an overall size of 2.91 Gb, utilizing PacBio high-fidelity (HiFi) sequencing complemented by Hi-C sequencing technology. The assembly is characterized by near-complete chromosomes, telomeres, and less gaps. Utilizing this highly quality assembly, we explored the phylogenetic relationship and speciation time. The gene family and selection signatures analyses indicated that candidate genes and biosynthetic pathways potentially contributing to disease immunity and thermotolerance of indicine cattle. Altogether, this study enriches the bovine pangenome repository and advances our understanding of the complex evolutionary patterns and distinctive adaptation traits of Chinese indicine cattle.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12895351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145642461","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 analysis of toxic Papilionidae butterflies utilizing aristolochic acid, Pachliopta aristolochiae, and Byasa alcinous. 利用马兜铃酸、马兜铃Pachliopta马兜铃酸和Byasa alcinous对有毒凤蝶进行全基因组分析。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsaf038

Shinya Komata, Rei Kajitani, Takahiro Yamabe, Tasuku Kitamura, Atsushi Toyoda, Tetsuya Kojima, Takehiko Itoh, Haruhiko Fujiwara

{"title":"Whole genome analysis of toxic Papilionidae butterflies utilizing aristolochic acid, Pachliopta aristolochiae, and Byasa alcinous.","authors":"Shinya Komata, Rei Kajitani, Takahiro Yamabe, Tasuku Kitamura, Atsushi Toyoda, Tetsuya Kojima, Takehiko Itoh, Haruhiko Fujiwara","doi":"10.1093/dnares/dsaf038","DOIUrl":"10.1093/dnares/dsaf038","url":null,"abstract":"Several species of toxic butterflies are known, including those from the Troidini tribe of the Papilionidae, which accumulate aristolochic acid from their host plants in Aristolochiae. However, the molecular mechanisms involved in utilizing aristolochic acid remain unknown. Toxic butterflies often exhibit warning colouration to signal their toxicity to predators, a complex adaptive trait with toxin utilization. In this study, we sequenced, assembled, and annotated the genomes of 2 toxic Troidini butterflies, Pachliopta aristolochiae (312.1 Mb, 13,497 genes) and Byasa alcinous (257.6 Mb, 14,669 genes), and conducted comparative genomics to identify genes involved in toxin utilization and warning colouration. Comparative analysis across 11 species revealed 31 gene families significantly expanded and 417 genes under positive selection. Additionally, 442 genes were highly expressed in the red spots on the hindwings of P. aristolochiae. The genes shared within these lists may be involved in the formation of the complex adaptive traits of toxin utilization and warning colouration. Functional analysis using RNAi confirmed the involvement of ebony, laccase2, and tyrosine hydroxylase (TH) in warning colouration. This research marks a significant starting point in understanding the genetic basis of aristolochic acid utilization and the formation of warning colouration, providing the first list of candidate genes.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12784068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145805367","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 genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies. 利用长读测序和单花粉基因分型技术对大理石豆染色体规模基因组进行组装。

IF 2.9 2区生物学

DNA Research Pub Date : 2026-01-09 DOI: 10.1093/dnares/dsag001

Kenta Shirasawa, Kazutoshi Yoshitake, Haruka Kondo, Shinji Kikuchi, Keiichiro Koiwai, Sota Fujii

{"title":"Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies.","authors":"Kenta Shirasawa, Kazutoshi Yoshitake, Haruka Kondo, Shinji Kikuchi, Keiichiro Koiwai, Sota Fujii","doi":"10.1093/dnares/dsag001","DOIUrl":"10.1093/dnares/dsag001","url":null,"abstract":"Malcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with the aim of understanding the molecular mechanisms underlying key traits in M. littorea, we present a de novo genome assembly consisting of 10 chromosome-scale sequences. We employed a high-fidelity long-read sequencing technology for genome assembly. To anchor the sequences to chromosomes, we developed a single-pollen genotyping method to construct a genetic linkage map based on SNPs derived from transcriptomes of pollen grains, possessing recombinant haploid genomes. We built a genome assembly consisting of 10 chromosome-scale sequences (215 Mb in total) for M. littorea containing 30,266 predicted genes. A comparative genome analysis and gene prediction indicated that the genome of M. littorea is double the size of the Arabidopsis thaliana genome, consistent with a whole-genome duplication followed by gene subfunctionalization and/or neofunctionalization in M. littorea. This study provides a basis for research on M. littorea, an understudied species with ecological and evolutionary significance.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145936055","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}

引用次数: 0

Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales. 真菌目Sordariales中全基因组密码子使用偏向的模式和驱动因素。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf036

Noah Hensen, Markus Hiltunen Thorén, Hanna Johannesson

引用次数: 0

MedakaBase as a unified genomic resource platform for medaka fish biology. MedakaBase是medaka鱼类生物学的统一基因组资源平台。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-12-01 DOI: 10.1093/dnares/dsaf030

Kenji Morikami, Yasuhiro Tanizawa, Masaru Yagura, Mika Sakamoto, Shoko Kawamoto, Yasukazu Nakamura, Katsushi Yamaguchi, Shuji Shigenobu, Kiyoshi Naruse, Satoshi Ansai, Shigehiro Kuraku

{"title":"MedakaBase as a unified genomic resource platform for medaka fish biology.","authors":"Kenji Morikami, Yasuhiro Tanizawa, Masaru Yagura, Mika Sakamoto, Shoko Kawamoto, Yasukazu Nakamura, Katsushi Yamaguchi, Shuji Shigenobu, Kiyoshi Naruse, Satoshi Ansai, Shigehiro Kuraku","doi":"10.1093/dnares/dsaf030","DOIUrl":"10.1093/dnares/dsaf030","url":null,"abstract":"Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3' untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.","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/PMC12666381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145349646","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