DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献

Telomere-to-telomere genome assembly of Oldenlandia diffusa 端粒-端粒基因组的奥登兰草（Oldenlandia diffusa）组装

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2024-04-11 DOI: 10.1093/dnares/dsae012

Yubang Gao, Dan Dan Xu, Zehua Hu

引用次数: 0

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum 基因组和转录组分析揭示了参与木槿花瓣表皮细胞细脊形成的基因

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2023-05-24 DOI: 10.1101/2023.05.23.541865

Shizuka Koshimizu, Sachiko Masuda, Arisa Shibata, Takayoshi Ishii, K. Shirasu, A. Hoshino, Masanori Arita

引用次数: 0

Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain) 西班牙巴利阿里群岛利尔福德壁虎Podarcis lilfordi (g<s:1> nther, 1874)的染色体水平基因组组装

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2023-02-15 DOI: 10.1101/2023.02.15.528647

J. Gómez-Garrido, F. Cruz, T. Alioto, Nathalie Feiner, T. Uller, M. Gut, Ignacio Sanchez Escudero, G. Tavecchia, A. Rotger, Katherin Eliana Otalora Acevedo, L. Baldo

{"title":"Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)","authors":"J. Gómez-Garrido, F. Cruz, T. Alioto, Nathalie Feiner, T. Uller, M. Gut, Ignacio Sanchez Escudero, G. Tavecchia, A. Rotger, Katherin Eliana Otalora Acevedo, L. Baldo","doi":"10.1101/2023.02.15.528647","DOIUrl":"https://doi.org/10.1101/2023.02.15.528647","url":null,"abstract":"The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes, assigning 72% to known functions. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85931951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Mituru Takanami, 1929–2022

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac046

引用次数: 0

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan 在日本驯化的红紫苏(perilla frutescens)的高度连续基因组组装

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-11-10 DOI: 10.1101/2022.09.16.508052

Keita Tamura, Mika Sakamoto, Yasuhiro Tanizawa, T. Mochizuki, S. Matsushita, Yoshihiro Kato, T. Ishikawa, Keisuke Okuhara, Yasukazu Nakamura, H. Bono

{"title":"A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan","authors":"Keita Tamura, Mika Sakamoto, Yasuhiro Tanizawa, T. Mochizuki, S. Matsushita, Yoshihiro Kato, T. Ishikawa, Keisuke Okuhara, Yasukazu Nakamura, H. Bono","doi":"10.1101/2022.09.16.508052","DOIUrl":"https://doi.org/10.1101/2022.09.16.508052","url":null,"abstract":"Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology. Here, we generated a high-quality genome assembly of red perilla domesticated in Japan. A near-complete chromosome level assembly of P. frutescens was generated contigs with N50 of 41.5 Mb from PacBio HiFi reads. 99.2% of the assembly was anchored into 20 pseudochromosomes, among which seven pseudochromosomes consisted of one contig, while the rest consisted of less than six contigs. Gene annotation and prediction of the sequences successfully predicted 86,258 gene models, including 76,825 protein-coding genes. Further analysis showed that potential targets of genome editing for the engineering of anthocyanin pathways in P. frutescens are located on the late-stage pathways. Overall, our genome assembly could serve as a valuable reference for selecting target genes for genome editing of P. frutescens.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75465530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake) 松茸(口蘑)端粒-端粒基因组组装的研究

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-07-25 DOI: 10.1101/2022.07.25.501483

Hiroyuki Kurokochi, Naoyuki Tajima, Mitsuhiko P. Sato, K. Yoshitake, S. Asakawa, S. Isobe, K. Shirasawa

{"title":"Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)","authors":"Hiroyuki Kurokochi, Naoyuki Tajima, Mitsuhiko P. Sato, K. Yoshitake, S. Asakawa, S. Isobe, K. Shirasawa","doi":"10.1101/2022.07.25.501483","DOIUrl":"https://doi.org/10.1101/2022.07.25.501483","url":null,"abstract":"Here, we report the first telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake), which consists of 13 chromosomes (spanning 160.7 Mb) and a 76 kb circular mitochondrial genome. The chromosome sequences were supported with telomeric repeats at the ends. GC-rich regions are located at the middle of the chromosomes and are enriched with long interspersed nuclear elements (LINEs). Repetitive sequences including long-terminal repeats (LTRs) and LINEs occupy 71.7% of the genome. A total of 28,322 potential protein-coding genes and 324 tRNA genes were predicted. Sequence and structure variant analysis revealed 2,322,349 single nucleotide polymorphisms and 102,831 insertions and deletions, 0.6% of which disrupted gene structure and function and were therefore classified as deleterious mutations. As many as 683 copies of the LTR retrotransposon MarY1 were detected in the matsutake genome, 91 of which were inserted in gene sequences. In addition, 187 sequence variations were found in the mitochondrial genome. The genomic data reported in this study would serve as a great reference for exploring the genetics and genomics of matsutake in the future, and the information gained would ultimately facilitate the conservation of this vulnerable genetic resource.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73031896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica 拟内寄生蜂Asobara japonica全基因组测序分析及RNA干扰方案

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-10 DOI: 10.1093/dnares/dsac019

Takumi Kamiyama, Yuko Shimada-Niwa, Hiroyuki Tanaka, M. Katayama, Takayoshi Kuwabara, Hitoha Mori, A. Kunihisa, T. Itoh, A. Toyoda, R. Niwa

{"title":"Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica","authors":"Takumi Kamiyama, Yuko Shimada-Niwa, Hiroyuki Tanaka, M. Katayama, Takayoshi Kuwabara, Hitoha Mori, A. Kunihisa, T. Itoh, A. Toyoda, R. Niwa","doi":"10.1093/dnares/dsac019","DOIUrl":"https://doi.org/10.1093/dnares/dsac019","url":null,"abstract":"Abstract Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75317345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Environmental DNA analysis for macro-organisms: species distribution and more 大型生物的环境DNA分析:物种分布等

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-01 DOI: 10.1093/dnares/dsac018

T. Minamoto

{"title":"Environmental DNA analysis for macro-organisms: species distribution and more","authors":"T. Minamoto","doi":"10.1093/dnares/dsac018","DOIUrl":"https://doi.org/10.1093/dnares/dsac018","url":null,"abstract":"Abstract In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81986643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production 全球调节因子AbrB的组成性表达恢复了基因组减少的枯草芽孢杆菌菌株的生长缺陷，并提高了其代谢物的产量

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-05-24 DOI: 10.1093/dnares/dsac015

Junya Yamamoto, O. Chumsakul, Yoshihiro Toya, T. Morimoto, Shenghao Liu, K. Masuda, Y. Kageyama, T. Hirasawa, Fumio Matsuda, N. Ogasawara, H. Shimizu, Ken-Ichi Yoshida, T. Oshima, S. Ishikawa

{"title":"Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production","authors":"Junya Yamamoto, O. Chumsakul, Yoshihiro Toya, T. Morimoto, Shenghao Liu, K. Masuda, Y. Kageyama, T. Hirasawa, Fumio Matsuda, N. Ogasawara, H. Shimizu, Ken-Ichi Yoshida, T. Oshima, S. Ishikawa","doi":"10.1093/dnares/dsac015","DOIUrl":"https://doi.org/10.1093/dnares/dsac015","url":null,"abstract":"Abstract Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83222699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad 西部掌足蟾蜍的染色体水平组装、注释和分类

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-05-18 DOI: 10.1093/dnares/dsac013

H. C. Liedtke, F. Cruz, J. Gómez-Garrido, Diego Fuentes Palacios, M. Marcet-Houben, M. Gut, T. Alioto, T. Gabaldón, I. Gomez‐Mestre

{"title":"Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad","authors":"H. C. Liedtke, F. Cruz, J. Gómez-Garrido, Diego Fuentes Palacios, M. Marcet-Houben, M. Gut, T. Alioto, T. Gabaldón, I. Gomez‐Mestre","doi":"10.1093/dnares/dsac013","DOIUrl":"https://doi.org/10.1093/dnares/dsac013","url":null,"abstract":"Abstract Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75127546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1