DNA Research最新文献_第10页

Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. 杜氏灯塔水母的基因组组装和转录组学分析。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac047

Yoshinori Hasegawa, Takashi Watanabe, Reo Otsuka, Shigenobu Toné, Shin Kubota, Hideki Hirakawa

引用次数: 0

Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure. 淡水凤尾硅藻 Mayamaea pseudoterrestris 对铜暴露的快速转录组和生理变化。

IF 3.9 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac037

Shigekatsu Suzuki, Shuhei Ota, Takahiro Yamagishi, Akihiro Tuji, Haruyo Yamaguchi, Masanobu Kawachi

{"title":"Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure.","authors":"Shigekatsu Suzuki, Shuhei Ota, Takahiro Yamagishi, Akihiro Tuji, Haruyo Yamaguchi, Masanobu Kawachi","doi":"10.1093/dnares/dsac037","DOIUrl":"10.1093/dnares/dsac037","url":null,"abstract":"Diatoms function as major primary producers, accumulating large amounts of biomass in most aquatic environments. Given their rapid responses to changes in environmental conditions, diatoms are used for the biological monitoring of water quality and for performing ecotoxicological tests in aquatic ecosystems. However, the molecular basis for their toxicity to chemical compounds remains largely unknown. Here, we sequenced the genome of a freshwater diatom, Mayamaea pseudoterrestris NIES-4280, which has been proposed as an alternative strain of Navicula pelliculosa UTEX 664 for performing the Organisation for Economic Co-operation and Development ecotoxicological test. This study shows that M. pseudoterrestris has a small genome and carries the lowest number of genes among freshwater diatoms. The gene content of M. pseudoterrestris is similar to that of the model marine diatom, Phaeodactylum tricornutum. Genes related to cell motility, polysaccharide metabolism, oxidative stress alleviation, intracellular calcium signalling, and reactive compound detoxification showed rapid changes in their expression patterns in response to copper exposure. Active gliding motility was observed in response to copper addition, and copper exposure decreased intracellular calcium concentration. These findings enhance our understanding of the environmental adaptation of diatoms, and elucidate the molecular basis of toxicity of chemical compounds in algae.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":3.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/08/11/dsac037.PMC9724779.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10403431","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

Correction to: The genome of Prunus humilis provides new insights to drought adaption and population diversity. 修正:李(Prunus humilis)的基因组为干旱适应和种群多样性提供了新的见解。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac038

引用次数: 0

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. 一种种间杂交食用葡萄“Shine Muscat”从头开始全基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac040

Kenta Shirasawa, Hideki Hirakawa, Akifumi Azuma, Fumiya Taniguchi, Toshiya Yamamoto, Akihiko Sato, Andrea Ghelfi, Sachiko N Isobe

{"title":"De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'.","authors":"Kenta Shirasawa, Hideki Hirakawa, Akifumi Azuma, Fumiya Taniguchi, Toshiya Yamamoto, Akihiko Sato, Andrea Ghelfi, Sachiko N Isobe","doi":"10.1093/dnares/dsac040","DOIUrl":"https://doi.org/10.1093/dnares/dsac040","url":null,"abstract":"The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10760482","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: 1

Chromosome-level genome of a leaf vegetable Glebionis coronaria provides insights into the biosynthesis of monoterpenoids contributing to its special aroma. 叶菜新冠Glebionis coronaria的染色体水平基因组为其特殊香气的单萜类化合物的生物合成提供了见解。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac036

Sen Wang, Anqi Wang, Hengchao Wang, Fan Jiang, Dong Xu, Wei Fan

{"title":"Chromosome-level genome of a leaf vegetable Glebionis coronaria provides insights into the biosynthesis of monoterpenoids contributing to its special aroma.","authors":"Sen Wang, Anqi Wang, Hengchao Wang, Fan Jiang, Dong Xu, Wei Fan","doi":"10.1093/dnares/dsac036","DOIUrl":"10.1093/dnares/dsac036","url":null,"abstract":"Glebionis coronaria is a popular vegetable with special aroma and a medical plant in East Asia and Mediterranean, but its biological studies and breeding have been hindered by the lack of reference genome. Here, we present a chromosome-level reference genome of G. coronaria, with assembled genome size of 6.8 Gb, which is the largest among all the published genomes of diploid Asteraceae species. The large genome size of G. coronaria is mainly caused by the recent widespread explosions of long-terminal-repeat retrotransposons. Analyses of macro-synteny and synonymous mutation rate distribution indicate that the G. coronaria genome experienced a whole-genome triplication at 40-45 million years ago, shared with all Asteraceae species. In subtribe Artemisiinae, Glebionis arose before the divergence of Chrysanthemum from Artemisia, and Glebionis species evolved much faster than Chrysanthemum and Artemisia species. In G. coronaria, the synthesis genes of monoterpenoids 8-oxocitronellyl enol and isopiperitenone were expanded, and the higher expressions of these expanded genes in leaves and stems may contribute to its special aroma. The G. coronaria genomic resources will promote the evolution studies of Asteraceae, the metabolism mechanism studies of bioactive compounds, and the breeding improvement of agronomic traits in G. coronaria.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10403430","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: 4

De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. 药用植物大叶龙胆的基因组组装为环烯醚萜类化合物的基因组进化和生物合成提供了新的见解。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac034

Tao Zhou, Guoqing Bai, Yiheng Hu, Markus Ruhsam, Yanci Yang, Yuemei Zhao

{"title":"De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids.","authors":"Tao Zhou, Guoqing Bai, Yiheng Hu, Markus Ruhsam, Yanci Yang, Yuemei Zhao","doi":"10.1093/dnares/dsac034","DOIUrl":"https://doi.org/10.1093/dnares/dsac034","url":null,"abstract":"Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/30/92/dsac034.PMC9724787.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10416325","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: 6

Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. 乌拉尔甘草染色体基因组组装揭示了以代谢基因簇为中心的特化代谢物生物合成。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac043

Amit Rai, Hideki Hirakawa, Megha Rai, Yohei Shimizu, Kenta Shirasawa, Shinji Kikuchi, Hikaru Seki, Mami Yamazaki, Atsushi Toyoda, Sachiko Isobe, Toshiya Muranaka, Kazuki Saito

{"title":"Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis.","authors":"Amit Rai, Hideki Hirakawa, Megha Rai, Yohei Shimizu, Kenta Shirasawa, Shinji Kikuchi, Hikaru Seki, Mami Yamazaki, Atsushi Toyoda, Sachiko Isobe, Toshiya Muranaka, Kazuki Saito","doi":"10.1093/dnares/dsac043","DOIUrl":"https://doi.org/10.1093/dnares/dsac043","url":null,"abstract":"A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis), a widely used herbal and natural medicine. The entire genome assembly was achieved in eight chromosomes, with contig and scaffold N50 as 36.02 and 60.2 Mb, respectively. With only 17 assembly gaps and half of the chromosomes having no or one assembly gap, the presented genome assembly is among the best plant genomes to date. Our results showed an advantage of using highly accurate long-read HiFi sequencing data for assembling a highly heterozygous genome including its complexed repeat content. Additionally, our analysis revealed that G. uralensis experienced a recent whole-genome duplication at approximately 59.02 million years ago post a gamma (γ) whole-genome triplication event, which contributed to its present chemotype features. The metabolic gene cluster analysis identified 355 gene clusters, which included the entire biosynthesis pathway of glycyrrhizin. The genome assembly and its annotations provide an essential resource for licorice improvement through molecular breeding and the discovery of valuable genes for engineering bioactive components and understanding the evolution of specialized metabolites biosynthesis.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9763095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10422694","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: 2

Improved assembly and annotation of the sesame genome. 改进芝麻基因组的组装和注释。

IF 3.9 2区生物学

DNA Research Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac041

Mingcheng Wang, Jianwei Huang, Song Liu, Xiaofeng Liu, Rui Li, Junjia Luo, Zhixi Fu

{"title":"Improved assembly and annotation of the sesame genome.","authors":"Mingcheng Wang, Jianwei Huang, Song Liu, Xiaofeng Liu, Rui Li, Junjia Luo, Zhixi Fu","doi":"10.1093/dnares/dsac041","DOIUrl":"10.1093/dnares/dsac041","url":null,"abstract":"Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here, we reported a high-quality, reference-level sesame genome assembly by integrating PacBio high-fidelity sequencing and Hi-C technology. Our updated sesame assembly was 309.35 Mb in size with a high chromosome anchoring rate (97.54%) and contig N50 size (13.48 Mb), which were better than previously published genomes. We identified 163.38 Mb repetitive elements and 24,345 high-confidence protein-coding genes in the updated sesame assembly. Comparative genomic analysis showed that sesame shared an ancient whole-genome duplication event with two Lamiales species. A total of 2,782 genes were tandemly duplicated. We also identified several genes that were likely involved in fatty acid and triacylglycerol biosynthesis. Our improved sesame assembly and annotation will facilitate future genetic studies and genomics-assisted breeding of sesame.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 6","pages":""},"PeriodicalIF":3.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10710794","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 of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea. Pendlebury's roundleaf bat（Hipposideros pendleburyi）的基因组组装揭示了 Tc1/Mariner DNA 转座子在 Rhinolophoidea 中的扩展。

IF 3.9 2区生物学

DNA Research Pub Date : 2022-08-23 DOI: 10.1093/dnares/dsac026

Wanapinun Nawae, Chutima Sonthirod, Thippawan Yoocha, Pitchaporn Waiyamitra, Pipat Soisook, Sithichoke Tangphatsornruang, Wirulda Pootakham

{"title":"Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea.","authors":"Wanapinun Nawae, Chutima Sonthirod, Thippawan Yoocha, Pitchaporn Waiyamitra, Pipat Soisook, Sithichoke Tangphatsornruang, Wirulda Pootakham","doi":"10.1093/dnares/dsac026","DOIUrl":"10.1093/dnares/dsac026","url":null,"abstract":"Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb with a scaffold N50 length of 15,398,518 bases. Our phylogenetic analysis placed H. pendleburyi within the rhinolophoid clade of the suborder Yinpterochiroptera. A synteny analysis showed that H. pendleburyi shared conserved chromosome segments (up to 105 Mb) with Rhinolophus ferrumequinum and Phyllostomus discolor albeit having different chromosome numbers and belonging different families. We found positive selection signals in genes involved in inflammation, spermatogenesis and Wnt signalling. The analyses of transposable elements suggested the contraction of short interspersed nuclear elements (SINEs) and the accumulation of young mariner DNA transposons in the analysed hipposiderids. Distinct mariners were likely horizontally transferred to hipposiderid genomes over the evolution of this family. The lineage-specific profiles of SINEs and mariners might involve in the evolution of hipposiderids and be associated with the phylogenetic separations of these bats from other bat families.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/86/08/dsac026.PMC9549598.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33497015","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 Prunus humilis provides new insights to drought adaption and population diversity. 李(Prunus humilis)基因组对干旱适应和种群多样性研究提供了新的见解。

IF 4.1 2区生物学

DNA Research Pub Date : 2022-06-25 DOI: 10.1093/dnares/dsac021

Yi Wang, Jun Xie, Hongna Zhang, Weidong Li, Zhanjun Wang, Huayang Li, Qian Tong, Gaixia Qiao, Yujuan Liu, Ying Tian, Yongzan Wei, Ping Li, Rong Wang, Weiping Chen, Zhengchang Liang, Meilong Xu

{"title":"The genome of Prunus humilis provides new insights to drought adaption and population diversity.","authors":"Yi Wang, Jun Xie, Hongna Zhang, Weidong Li, Zhanjun Wang, Huayang Li, Qian Tong, Gaixia Qiao, Yujuan Liu, Ying Tian, Yongzan Wei, Ping Li, Rong Wang, Weiping Chen, Zhengchang Liang, Meilong Xu","doi":"10.1093/dnares/dsac021","DOIUrl":"https://doi.org/10.1093/dnares/dsac021","url":null,"abstract":"Prunus humilis (2n = 2x = 16) is a dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, PacBio and HiC sequencing technologies. This genome was 254.38 Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at ∼ 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, and more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis that could be used as a potential model plant for horticultural research.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"29 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10412596","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: 3