DNA Research最新文献

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 : 2025-10-09 DOI: 10.1093/dnares/dsaf027

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

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 : 2025-10-07 DOI: 10.1093/dnares/dsaf028

Dorinda Torres-Sabino, Andrés Blanco, 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, Paula R Villamayor, Inmaculada Rasines, Ignacio Martín, Carmen Bouza, Diego Robledo, Paulino Martínez","doi":"10.1093/dnares/dsaf028","DOIUrl":"https://doi.org/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":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Satellite DNAs rising from the transposon graveyards. 从转座子墓地升起的卫星dna。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-30 DOI: 10.1093/dnares/dsaf026

Eva Šatović-Vukšić, Patrik Majcen, Miroslav Plohl

{"title":"Satellite DNAs rising from the transposon graveyards.","authors":"Eva Šatović-Vukšić, Patrik Majcen, Miroslav Plohl","doi":"10.1093/dnares/dsaf026","DOIUrl":"https://doi.org/10.1093/dnares/dsaf026","url":null,"abstract":"Repetitive DNA sequences, as transposable elements (TEs) and satellite DNA (satDNA) spread and diversify within host genomes, impacting genome biology in numerous ways. In the first part of this review, we emphasize the evolutionary importance of satDNAs and TEs, providing a short summary of their roles and the mechanisms by which they influence the structure and function of genomes. We also discuss the broad, complex, and extensive relationships between TEs and satDNAs. Following that, we bring together different mechanisms on the generation of satDNA from TE, as it has been demonstrated that almost any part of any type of TE can undergo tandemization and produce novel satDNAs. Importantly, we here present a hypothesis that would explain the existence of particular types of monomers, namely composite satDNA monomers which display multiple subsequent stretches of similarity to various TEs, for which the explanation was lacking so far. We propose that even highly shuffled and degraded TE remnants residing in heterochromatin \"TE graveyards\" can give rise to new satDNA sequence monomers, transforming these genomic loci into DNA \"recycling yards.\" Furthermore, we emphasize important evolutionary questions regarding the causes, mechanisms, and frequency of these occurrences.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193183","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

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 : 2025-09-16 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":"https://doi.org/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 analyzed substitution rates between bases, both unmethylated and methylated ones. As the model methylomes, we chose those of Helicobacter pylori, an 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 work represents the first step towards molecular evolutionary epigenomics, which, we expect, would contribute to understanding epigenome evolution.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 2025-09-15 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":"https://doi.org/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 non-linear 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: modeling 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. Toward the end, we propose a future direction centered 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":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Localization of the origin of transfer (oriT) for Salmonella Genomic Island 4 (SGI-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 : 2025-09-15 DOI: 10.1093/dnares/dsaf023

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

{"title":"Localization of the origin of transfer (oriT) for Salmonella Genomic Island 4 (SGI-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":"https://doi.org/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: a) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and b) 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":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history. 对红杜鹃（Sauvagesia rhodoleuca）染色体尺度的基因组组装为其基因组进化和人口统计学历史提供了新的认识。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf022

Tian-Wen Xiao, Xin-Feng Wang, Zheng-Feng Wang, Hai-Fei Yan

{"title":"Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.","authors":"Tian-Wen Xiao, Xin-Feng Wang, Zheng-Feng Wang, Hai-Fei Yan","doi":"10.1093/dnares/dsaf022","DOIUrl":"10.1093/dnares/dsaf022","url":null,"abstract":"Sauvagesia rhodoleuca is an endangered species endemic to southern China. Due to human activities, only 6 fragmented populations remain in Guangdong and Guangxi. Despite considerable conservation efforts, its demographic history and evolution remain poorly understood, particularly from a genomic perspective. To address this, we assembled a chromosome-scale genome of S. rhodoleuca using Nanopore long-read sequencing, DNA short-read sequencing, RNA-seq, and Hi-C data. A total of 290.37 Mb of assembled sequences, accounting for 99.76% of the genome, were successfully anchored to 19 pseudo-chromosomes, achieving a BUSCO completeness of 98.40% and a long terminal repeat assembly index of 17.28. Genome annotation identified 26,758 protein-coding genes and 369 tRNA genes. Demographic analysis revealed a sharp decline in the effective population size of S. rhodoleuca beginning approximately 1 million years ago. Whole-genome duplication (WGD) analysis revealed that S. rhodoleuca experienced a whole-genome triplication (WGT) followed by a more recent WGD after diverging from the Rhizophoraceae. Genes retained from WGT and WGD events played key roles in the development and survival of S. rhodoleuca, as indicated by Gene Ontology analysis. The high-quality genome of S. rhodoleuca provides insights into its genomic characteristics and evolutionary history, offering a valuable resource for conservation and genetic management.","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/PMC12448743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016517","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

Diversity, evolution, and transcription of endogenous retroviruses in Chiroptera genomes. 内生逆转录病毒在翼翅目基因组中的多样性、进化和转录。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf021

Zhi-Jian Zhou, Yang Xiao, Jie Fang, Yong-Xiu Yao, Chen-Hui Yang, Laurent Dacheux, Dong-Sheng Luo, Ye Qiu, Xing-Yi Ge

{"title":"Diversity, evolution, and transcription of endogenous retroviruses in Chiroptera genomes.","authors":"Zhi-Jian Zhou, Yang Xiao, Jie Fang, Yong-Xiu Yao, Chen-Hui Yang, Laurent Dacheux, Dong-Sheng Luo, Ye Qiu, Xing-Yi Ge","doi":"10.1093/dnares/dsaf021","DOIUrl":"10.1093/dnares/dsaf021","url":null,"abstract":"Bats (Chiroptera) are a taxonomic group of immense biological and ecological importance. They are primary reservoirs and carriers of various zoonotic viruses. Endogenous retroviruses (ERVs) originate from ancient retroviruses invading the host, and ERV-derived sequences can function as regulatory elements which influence gene expression and contribute to both physiological and pathological processes. However, ERVs and ERV-like elements (ERVLEs) carried by bats have not been fully characterized. In this study, we systematically explored the ERVs in 61 bat species and identified 10,352 bat-ERVs and 5,884 bat-ERVLEs sequences, and these sequences covered 3 major virus genera and included 7 groups related to human ERVs in the subfamily Orthoretrovirinae. In particular, a relatively intact endogenous deltaretrovirus sequence was identified in Molossus molossus. Additionally, 358 bat-ERV and 33 bat-ERVLE were identified as recombinants. The integration time of bat-ERVs was estimated to be concentrated in the last 10 to 40 million years, indicating their role in shaping the bat genome during the long-term co-evolution of virus and host. Furthermore, carnivorous bats tended to have more relatively complete and younger ERVs compared to herbivorous bats. According to bat transcriptomes, we found that 1,385 bat-ERVs and 197 bat-ERVLEs had transcriptional potential in 20 different tissues of 25 bats, implying that bat-ERVs harboured actively expressed genes with potential functions. In summary, we comprehensively characterized bat-ERVs in terms of their evolution, types and potential functions, providing foundational data and a new perspective for further research on bat-ERVs.","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/PMC12402889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977606","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 survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference. 八种黄龙属植物的基因组调查和进化分析：SSR分析、线粒体特征和种群动态推断。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf020

Min Jiang, Qi Liu, Chao Jiang, Mingfei Zhan, Haibo Wen, Fengyue Shu, Lingli Xie, Tengteng Liu, Chenliang Ren, Wenqiao Tang, Kai Liu

{"title":"Genome survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference.","authors":"Min Jiang, Qi Liu, Chao Jiang, Mingfei Zhan, Haibo Wen, Fengyue Shu, Lingli Xie, Tengteng Liu, Chenliang Ren, Wenqiao Tang, Kai Liu","doi":"10.1093/dnares/dsaf020","DOIUrl":"10.1093/dnares/dsaf020","url":null,"abstract":"Freshwater bivalves are vital to aquatic ecosystems but face severe global threats. Understanding their genomic traits and evolution is crucial for effective conservation. This study conducted whole-genome sequencing on 8 Lamprotula species. These 8 species exhibited high genomic complexity, characterized by large genomes (1.89 to 2.65 Gb), high heterozygosity (>0.8), and high repeat content (>60%), estimated by k-mer analysis. Genome assemblies showed that L. caveata had the largest genome, while L. polysticta had the smallest. Furthermore, the assembled genome sizes of these 8 species exhibited an average increase of 22.58% compared to k-mer analysis estimates, largely due to their high heterozygosity. The mitochondrial genomes of these 8 species ranged in size from 15.69 kb to 17.13 kb, with GC contents varying from 36.36% to 40.77%. Phylogenetic analysis indicated early divergence of L. leai and L. caveata from the other 6 species. Pairwise Sequentially Markovian Coalescent analysis revealed population bottlenecks over the past million years, with L. rochechouarti showing more significant population size fluctuations during the Pleistocene Glacial Epoch. In summary, this study provides comprehensive genomic insights into 8 Lamprotula species, highlighting their high genomic complexity and evolutionary divergence, thereby establishing a crucial foundation for future conservation and genetic research efforts.","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/PMC12454935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838502","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

Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2. 基于参考的日本大麦（Hordeum vulgare ssp）染色体规模组装。Hayakiso的变种；

IF 3.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 10.1093/dnares/dsaf016

Tsuyoshi Tanaka, Yuhi Haraguchi, Takatomo Todoroki, Daisuke Saisho, Tomomi Abiko, Hiroomi Kai

{"title":"Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.","authors":"Tsuyoshi Tanaka, Yuhi Haraguchi, Takatomo Todoroki, Daisuke Saisho, Tomomi Abiko, Hiroomi Kai","doi":"10.1093/dnares/dsaf016","DOIUrl":"10.1093/dnares/dsaf016","url":null,"abstract":"Current advances in next-generation sequencing (NGS) technology and assembling programs permit construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex'. We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B, and D homoeologs, respectively), and rice. From the gene ontology analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as 'response to biotic and abiotic stress' and 'metabolic process'. Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512763","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