DNA Research最新文献_第7页

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). 甜菜EL10 (Beta vulgaris L.)的连续从头基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac033

J Mitchell McGrath, Andrew Funk, Paul Galewski, Shujun Ou, Belinda Townsend, Karen Davenport, Hajnalka Daligault, Shannon Johnson, Joyce Lee, Alex Hastie, Aude Darracq, Glenda Willems, Steve Barnes, Ivan Liachko, Shawn Sullivan, Sergey Koren, Adam Phillippy, Jie Wang, Tiffany Liu, Jane Pulman, Kevin Childs, Shengqiang Shu, Anastasia Yocum, Damian Fermin, Effie Mutasa-Göttgens, Piergiorgio Stevanato, Kazunori Taguchi, Rachel Naegele, Kevin Dorn

{"title":"A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).","authors":"J Mitchell McGrath, Andrew Funk, Paul Galewski, Shujun Ou, Belinda Townsend, Karen Davenport, Hajnalka Daligault, Shannon Johnson, Joyce Lee, Alex Hastie, Aude Darracq, Glenda Willems, Steve Barnes, Ivan Liachko, Shawn Sullivan, Sergey Koren, Adam Phillippy, Jie Wang, Tiffany Liu, Jane Pulman, Kevin Childs, Shengqiang Shu, Anastasia Yocum, Damian Fermin, Effie Mutasa-Göttgens, Piergiorgio Stevanato, Kazunori Taguchi, Rachel Naegele, Kevin Dorn","doi":"10.1093/dnares/dsac033","DOIUrl":"https://doi.org/10.1093/dnares/dsac033","url":null,"abstract":"A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9896481/pdf/dsac033.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9208990","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 methanogen core and pangenome: conservation and variability across biology's growth temperature extremes. 甲烷发生器核心和泛基因组：生物生长温度极值的保护和变异。

IF 3.9 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac048

Paula Prondzinsky, Sakae Toyoda, Shawn Erin McGlynn

{"title":"The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes.","authors":"Paula Prondzinsky, Sakae Toyoda, Shawn Erin McGlynn","doi":"10.1093/dnares/dsac048","DOIUrl":"10.1093/dnares/dsac048","url":null,"abstract":"Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part because of the unique constraints among different evolutionary lineages and physiological groups. Here we compared the genomes of cultivated psychrotolerant and thermotolerant methanogens, which are physiologically related and span growth temperatures from -2.5°C to 122°C. Despite being phylogenetically distributed amongst three phyla in the archaea, the genomic core of cultivated methanogens comprises about one-third of a given genome, while the genome fraction shared by any two organisms decreases with increasing phylogenetic distance between them. Increased methanogenic growth temperature is associated with reduced genome size, and thermotolerant organisms-which are distributed across the archaeal tree-have larger core genome fractions, suggesting that genome size is governed by temperature rather than phylogeny. Thermotolerant methanogens are enriched in metal and other transporters, and psychrotolerant methanogens are enriched in proteins related to structure and motility. Observed amino acid compositional differences between temperature groups include proteome charge, polarity and unfolding entropy. Our results suggest that in the methanogens, shared physiology maintains a large, conserved genomic core even across large phylogenetic distances and biology's temperature extremes.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9454071","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 a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'. 日本地方辣椒品种辣椒的染色体规模基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac052

Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Isobe

{"title":"Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.","authors":"Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Isobe","doi":"10.1093/dnares/dsac052","DOIUrl":"https://doi.org/10.1093/dnares/dsac052","url":null,"abstract":"Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of 'Takanotsume'. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3,058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34,324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e. chromosomal rearrangements and transposon-insertion polymorphisms) between 'Takanotsume' and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of 'Takanotsume'.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10591367","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

Characterization of proteogenomic signatures of differentiation of CD4+ T cell subsets. CD4+ T 细胞亚群分化的蛋白质基因组特征。

IF 3.9 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac054

Toshio Kanno, Ryo Konno, Keisuke Miyako, Takahiro Nakajima, Satoru Yokoyama, Shigemi Sasamoto, Hikari K Asou, Junichiro Ohzeki, Yusuke Kawashima, Yoshinori Hasegawa, Osamu Ohara, Yusuke Endo

{"title":"Characterization of proteogenomic signatures of differentiation of CD4+ T cell subsets.","authors":"Toshio Kanno, Ryo Konno, Keisuke Miyako, Takahiro Nakajima, Satoru Yokoyama, Shigemi Sasamoto, Hikari K Asou, Junichiro Ohzeki, Yusuke Kawashima, Yoshinori Hasegawa, Osamu Ohara, Yusuke Endo","doi":"10.1093/dnares/dsac054","DOIUrl":"10.1093/dnares/dsac054","url":null,"abstract":"Functionally distinct CD4+ helper T (Th) cell subsets, including Th1, Th2, Th17, and regulatory T cells (Treg), play a pivotal role in the regulation of acquired immunity. Although the key proteins involved in the regulation of Th cell differentiation have already been identified how the proteogenomic landscape changes during the Th cell activation remains unclear. To address this issue, we characterized proteogenomic signatures of differentiation to each Th cell subsets by RNA sequencing and liquid chromatography-assisted mass spectrometry, which enabled us to simultaneously quantify more than 10,000 protein-coding transcripts and 8,000 proteins in a single-shot. The results indicated that T cell receptor activation affected almost half of the transcript and protein levels in a low correlative and gene-specific manner, and specific cytokine treatments modified the transcript and protein profiles in a manner specific to each Th cell subsets: Th17 and Tregs particularly exhibited unique proteogenomic signatures compared to other Th cell subsets. Interestingly, the in-depth proteome data revealed that mRNA profiles alone were not enough to delineate functional changes during Th cell activation, suggesting that the proteogenomic dataset obtained in this study serves as a unique and indispensable data resource for understanding the comprehensive molecular mechanisms underlying effector Th cell differentiation.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156403","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

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae. 从玉米科第一个基因组序列看菊科植物的核型进化。

IF 4.1 2区生物学

DNA Research Pub Date : 2023-02-01 DOI: 10.1093/dnares/dsac051

Congcong Dong, Shang Wang, Han Zhang, Jianquan Liu, Minjie Li

{"title":"Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae.","authors":"Congcong Dong, Shang Wang, Han Zhang, Jianquan Liu, Minjie Li","doi":"10.1093/dnares/dsac051","DOIUrl":"https://doi.org/10.1093/dnares/dsac051","url":null,"abstract":"Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome-level genome for Cornus controversa. This was generated using high-fidelity plus Hi-C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8b/b1/dsac051.PMC9835862.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10594230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome assembly and 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