DNA Research最新文献_第2页

Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins. 单卵双生子间全基因组后体细胞突变的功能分布。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-10-01 DOI: 10.1093/dnares/dsae028

Kenichi Yamamoto, Yoko Lee, Tatsuo Masuda, Keiichi Ozono, Yoshinori Iwatani, Mikio Watanabe, Yukinori Okada, Norio Sakai

{"title":"Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins.","authors":"Kenichi Yamamoto, Yoko Lee, Tatsuo Masuda, Keiichi Ozono, Yoshinori Iwatani, Mikio Watanabe, Yukinori Okada, Norio Sakai","doi":"10.1093/dnares/dsae028","DOIUrl":"10.1093/dnares/dsae028","url":null,"abstract":"Monozygotic (MZ) twins originate from a single fertilized egg, making them genetically identical at the time of conception. However, postzygotic somatic mutations (PZMs) can introduce genetic differences after separation. Although whole-genome sequencing (WGS) sheds light on somatic mutations in cancer genomics, its application in genomic studies of MZ twins remains limited. In this study, we investigate PZMs in 30 healthy MZ twin pairs from the Osaka University Center for Twin Research using WGS (average depth = 23.8) and a robust germline-calling algorithm. We find high genotype concordance rates (exceeding 99%) in MZ twins. We observe an enrichment of PZMs with variant allele frequency around 0.5 in twins with highly concordant genotypes. These PZMs accumulate more frequently in non-coding regions compared with protein-coding regions, which could potentially influence gene expression. No significant association is observed between the number of PZMs and age or sex. Direct sequencing confirms a missense mutation in the ANKRD35 gene among the PZMs. By applying a genome-wide mutational signature pattern technique, we detect an age-related clock-like signature in these early postzygotic somatic mutations in MZ twins. Our study provides insights that contribute to a deeper understanding of genetic variation in MZ twins.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11472055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142300253","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

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum). 番茄（Solanum lycopersicum）模式栽培品种 Micro-Tom 在不同分布区的基因组变异。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-10-01 DOI: 10.1093/dnares/dsae016

Hideki Nagasaki, Kenta Shirasawa, Ken Hoshikawa, Sachiko Isobe, Hiroshi Ezura, Koh Aoki, Hideki Hirakawa

{"title":"Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).","authors":"Hideki Nagasaki, Kenta Shirasawa, Ken Hoshikawa, Sachiko Isobe, Hiroshi Ezura, Koh Aoki, Hideki Hirakawa","doi":"10.1093/dnares/dsae016","DOIUrl":"10.1093/dnares/dsae016","url":null,"abstract":"Micro-Tom is a cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarfism, and substantial EMS-mutagenized lines have been reported. After Micro-Tom was generated in Florida, USA, it was distributed to research institutes worldwide and used as a genetic resource. In Japan, the Micro-Tom lines have been genetically fixed; currently, three lines have been re-distributed from three institutes, but many phenotypes among the lines have been observed. We have determined the genome sequence de novo of the Micro-Tom KDRI line, one of the Micro-Tom lines distributed from Kazusa DNA Research Institute (KDRI) in Japan, and have built chromosome-scale pseudomolecules. Genotypes among six Micro-Tom lines, including three in Japan, one in the United States, one in France, and one in Brazil showed phenotypic alternation. Here, we unveiled the swift emergence of genetic diversity in both phenotypes and genotypes within the Micro-Tom genome sequence during its propagation. These findings offer valuable insights crucial for the management of bioresources.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285285","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

Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples. 推进苹果遗传学研究：Malus coronaria 和 Malus ioensis 基因组以及基于基因家族的北美本地苹果泛基因组。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-10-01 DOI: 10.1093/dnares/dsae026

Anže Švara, Honghe Sun, Zhangjun Fei, Awais Khan

{"title":"Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples.","authors":"Anže Švara, Honghe Sun, Zhangjun Fei, Awais Khan","doi":"10.1093/dnares/dsae026","DOIUrl":"10.1093/dnares/dsae026","url":null,"abstract":"Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern United States, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis, generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these 2 genomes and previously published genome of M. angustifolia, and lower relatedness with M. fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11489038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057178","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 medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies. 利用 Nanopore 和 Hi-C 技术进行药用昆虫 Blaps rhynchopetera 染色体级基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-09-09 DOI: 10.1093/dnares/dsae027

Wei Zhang,Yue Li,Qi Wang,Qun Yu,Yuchen Ma,Lei Huang,Chenggui Zhang,Zizhong Yang,Jiapeng Wang,Huai Xiao

{"title":"Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.","authors":"Wei Zhang,Yue Li,Qi Wang,Qun Yu,Yuchen Ma,Lei Huang,Chenggui Zhang,Zizhong Yang,Jiapeng Wang,Huai Xiao","doi":"10.1093/dnares/dsae027","DOIUrl":"https://doi.org/10.1093/dnares/dsae027","url":null,"abstract":"The Blaps rhynchopetera Fairmaire is a significant medicinal resource in southwestern China. We utilized Nanopore and Hi-C technologies in combination to generate a high-quality, chromosome-level assembly of the B. rhynchopetera genome and described its genetic features. Genome surveys revealed that B. rhynchopetera is a highly heterozygous species. The assembled genome was 379.24 Mb in size, of which 96.03% was assigned to 20 pseudochromosomes. A total of 212.93 Mb of repeat sequences were annotated and 26,824 protein-coding genes and 837 non-coding RNAs were identified. Phylogenetic analysis indicated that the divergence of the ancestors of B. rhynchopetera and its closely related species Tenebrio molitor at about 85.6 mya. The co-linearity analysis showed that some chromosomes of B. rhynchopetera may have happen fission events and it has a good synteny relationship with Tribolium castaneum. Furthermore, in the enrichment analyses, the gene families related to detoxification and immunity of B. rhynchopetera facilitated the understanding its environmental adaptations, which will serve as a valuable research resource for pest control strategies and conservation efforts of beneficial insects. This high-quality reference genome will also contribute to the conservation of insect species diversity and genetic resources.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"15 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206080","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

Pan-lineage Mycobacterium tuberculosis reference genome for enhanced molecular diagnosis. 用于强化分子诊断的全系结核分枝杆菌参考基因组。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae023

Kunhyung Bahk, Joohon Sung, Mitsuko Seki, Kyungjong Kim, Jina Kim, Hongjo Choi, Jake Whang, Satoshi Mitarai

{"title":"Pan-lineage Mycobacterium tuberculosis reference genome for enhanced molecular diagnosis.","authors":"Kunhyung Bahk, Joohon Sung, Mitsuko Seki, Kyungjong Kim, Jina Kim, Hongjo Choi, Jake Whang, Satoshi Mitarai","doi":"10.1093/dnares/dsae023","DOIUrl":"10.1093/dnares/dsae023","url":null,"abstract":"In Mycobacterium tuberculosis (MTB) control, whole genome sequencing-based molecular drug susceptibility testing (molDST-WGS) has emerged as a pivotal tool. However, the current reliance on a single-strain reference limits molDST-WGS's true potential. To address this, we introduce a new pan-lineage reference genome, 'MtbRf'. We assembled 'unmapped' reads from 3,614 MTB genomes (751 L1; 881 L2; 1,700 L3; and 282 L4) into 35 shared, annotated contigs (54 coding sequences [CDSs]). We constructed MtbRf through: (1) searching for contig homologues among genome database that precipitate results uniquely within Mycobacteria genus; (2) comparing genomes with H37Rv ('lift-over') to define 18 insertions; and (3) filling gaps in H37Rv with insertions. MtbRf adds 1.18% sequences to H37rv, salvaging >60% of previously unmapped reads. Transcriptomics confirmed gene expression of new CDSs. The new variants provided a moderate DST predictive value (AUROC 0.60-0.75). MtbRf thus unveils previously hidden genomic information and lays the foundation for lineage-specific molDST-WGS.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11339604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914498","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

A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China. 染色体水平的基因组组装揭示了中国黄河流域柽柳的地方适应性。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae021

Shuai Gong, Honghao Gan, Jianmin Chu, Zhaoshan Wang, Jia Sun

{"title":"A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China.","authors":"Shuai Gong, Honghao Gan, Jianmin Chu, Zhaoshan Wang, Jia Sun","doi":"10.1093/dnares/dsae021","DOIUrl":"10.1093/dnares/dsae021","url":null,"abstract":"Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472384","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

A high-quality genome assembly reveals adaptations underlying glossy, wax-coated leaves in the heat-tolerant wild raspberry Rubus leucanthus. 高质量的基因组组装揭示了耐热野生树莓 Rubus leucanthus 叶片光泽和蜡质涂层背后的适应性。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae024

Wei Wu, Longyuan Wang, Weicheng Huang, Xianzhi Zhang, Yongquan Li, Wei Guo

{"title":"A high-quality genome assembly reveals adaptations underlying glossy, wax-coated leaves in the heat-tolerant wild raspberry Rubus leucanthus.","authors":"Wei Wu, Longyuan Wang, Weicheng Huang, Xianzhi Zhang, Yongquan Li, Wei Guo","doi":"10.1093/dnares/dsae024","DOIUrl":"10.1093/dnares/dsae024","url":null,"abstract":"With glossy, wax-coated leaves, Rubus leucanthus is one of the few heat-tolerant wild raspberry trees. To ascertain the underlying mechanism of heat tolerance, we generated a high-quality genome assembly with a genome size of 230.9 Mb and 24,918 protein-coding genes. Significantly expanded gene families were enriched in the flavonoid biosynthesis pathway and the circadian rhythm-plant pathway, enabling survival in subtropical areas by accumulating protective flavonoids and modifying photoperiodic responses. In contrast, plant-pathogen interaction and MAPK signaling involved in response to pathogens were significantly contracted. The well-known heat response elements (HSP70, HSP90, and HSFs) were reduced in R. leucanthus compared to two other heat-intolerant species, R. chingii and R. occidentalis, with transcriptome profiles further demonstrating their dispensable roles in heat stress response. At the same time, three significantly positively selected genes in the pathway of cuticular wax biosynthesis were identified, and may contribute to the glossy, wax-coated leaves of R. leucanthus. The thick, leathery, waxy leaves protect R. leucanthus against pathogens and herbivores, supported by the reduced R gene repertoire in R. leucanthus (355) compared to R. chingii (376) and R. occidentalis (449). Our study provides some insights into adaptive divergence between R. leucanthus and other raspberry species on heat tolerance.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890803","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 and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758). 黑海胆 Arbacia lixula (Linnaeus, 1758) 染色体级基因组组装与注释。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae020

Carles Galià-Camps, Carlos Carreras, Marta Pascual, Carola Greve, Tilman Schell, Xavier Turon, Creu Palacín, Rocío Pérez-Portela, Owen S Wangensteen, Cinta Pegueroles

{"title":"Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758).","authors":"Carles Galià-Camps, Carlos Carreras, Marta Pascual, Carola Greve, Tilman Schell, Xavier Turon, Creu Palacín, Rocío Pérez-Portela, Owen S Wangensteen, Cinta Pegueroles","doi":"10.1093/dnares/dsae020","DOIUrl":"10.1093/dnares/dsae020","url":null,"abstract":"The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441107","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

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. 高完整性葛根变种叶基因组和种群分析揭示了葛根属的遗传多样性。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae017

Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan

{"title":"High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.","authors":"Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan","doi":"10.1093/dnares/dsae017","DOIUrl":"10.1093/dnares/dsae017","url":null,"abstract":"Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176847","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

Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea. 揭示 DNA 甲基化景观，解读鹰嘴豆表型多样性的进化足迹。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae013

Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida

{"title":"Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.","authors":"Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida","doi":"10.1093/dnares/dsae013","DOIUrl":"10.1093/dnares/dsae013","url":null,"abstract":"Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874953","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