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 high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. 高质量的单倍型阶段基因组重建揭示了珍珠牡蛎中意想不到的单倍型多样性。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-12-01 DOI: 10.1093/dnares/dsac035

Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, Kiyohito Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh, Eugene W Myers

{"title":"A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.","authors":"Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, Kiyohito Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh, Eugene W Myers","doi":"10.1093/dnares/dsac035","DOIUrl":"https://doi.org/10.1093/dnares/dsac035","url":null,"abstract":"Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9646362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40453216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

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

Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development. 丝豆染色体水平基因组为左旋多巴的合成研究和开发提供了资源。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-08-23 DOI: 10.1093/dnares/dsac031

Shijie Hao, Qijin Ge, Yunchang Shao, Benqin Tang, Guangyi Fan, Canyu Qiu, Xue Wu, Liangwei Li, Xiaochuan Liu, Chengcheng Shi, Simon Ming-Yuen Lee

{"title":"Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development.","authors":"Shijie Hao, Qijin Ge, Yunchang Shao, Benqin Tang, Guangyi Fan, Canyu Qiu, Xue Wu, Liangwei Li, Xiaochuan Liu, Chengcheng Shi, Simon Ming-Yuen Lee","doi":"10.1093/dnares/dsac031","DOIUrl":"https://doi.org/10.1093/dnares/dsac031","url":null,"abstract":"Mucuna pruriens, commonly called velvet bean, is the main natural source of levodopa (L-DOPA), which has been marketed as a psychoactive drug for the clinical management of Parkinson's disease and dopamine-responsive dystonia. Although velvet bean is a very important plant species for food and pharmaceutical manufacturing, the lack of genetic and genomic information about this species severely hinders further molecular research thereon and biotechnological development. Here, we reported the first velvet bean genome, with a size of 500.49 Mb and 11 chromosomes encoding 28,010 proteins. Genomic comparison among legume species indicated that velvet bean speciated ∼29 Ma from soybean clade, without specific genome duplication. Importantly, we identified 21 polyphenol oxidase coding genes that catalyse l-tyrosine to L-DOPA in velvet bean, and two subfamilies showing tandem expansion on Chr3 and Chr7 after speciation. Interestingly, disease-resistant and anti-pathogen gene families were found contracted in velvet bean, which might be related to the expansion of polyphenol oxidase. Our study generated a high-quality genomic reference for velvet bean, an economically important agricultural and medicinal plant, and the newly reported L-DOPA biosynthetic genes could provide indispensable information for the biotechnological and sustainable development of an environment-friendly L-DOPA biosynthesis processing method.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fb/d9/dsac031.PMC9479889.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40622672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. 洋葱全基因组标记设计流程的建立及其在基于靶扩增子测序的基因分型中的应用。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-08-23 DOI: 10.1093/dnares/dsac020

Daisuke Sekine, Satoshi Oku, Tsukasa Nunome, Hideki Hirakawa, Mai Tsujimura, Toru Terachi, Atsushi Toyoda, Masayoshi Shigyo, Shusei Sato, Hikaru Tsukazaki

{"title":"Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping.","authors":"Daisuke Sekine, Satoshi Oku, Tsukasa Nunome, Hideki Hirakawa, Mai Tsujimura, Toru Terachi, Atsushi Toyoda, Masayoshi Shigyo, Shusei Sato, Hikaru Tsukazaki","doi":"10.1093/dnares/dsac020","DOIUrl":"https://doi.org/10.1093/dnares/dsac020","url":null,"abstract":"Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9410872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40420492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle. 发育、幼年和成年日本黑牛31个组织中124个转录组的综合分析。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-08-23 DOI: 10.1093/dnares/dsac032

Taichi Arishima, Hiroyuki Wakaguri, Ryotaro Nakashima, Seigo Sakakihara, Keisuke Kawashima, Yoshikazu Sugimoto, Yutaka Suzuki, Shinji Sasaki

{"title":"Comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle.","authors":"Taichi Arishima, Hiroyuki Wakaguri, Ryotaro Nakashima, Seigo Sakakihara, Keisuke Kawashima, Yoshikazu Sugimoto, Yutaka Suzuki, Shinji Sasaki","doi":"10.1093/dnares/dsac032","DOIUrl":"https://doi.org/10.1093/dnares/dsac032","url":null,"abstract":"Omic analyses of economically important animals, including Japanese Black cattle, are currently underway worldwide. In particular, tissue and developmental stage-specific transcriptome characterization is essential for understanding the molecular mechanisms underlying the phenotypic expression of genetic disorders and economic traits. Here, we conducted a comprehensive analysis of 124 transcriptomes across 31 major tissues from fetuses, juvenile calves, and adult Japanese Black cattle using short-read sequencing. We found that genes exhibiting high tissue-specific expression tended to increase after 60 days from fertilization and significantly reflected tissue-relevant biology. Based on gene expression variation and inflection points during development, we categorized gene expression patterns as stable, increased, decreased, temporary, or complex in each tissue. We also analysed the expression profiles of causative genes (e.g. SLC12A1, ANXA10, and MYH6) for genetic disorders in cattle, revealing disease-relevant expression patterns. In addition, to directly analyse the structure of full-length transcripts without transcript reconstruction, we performed RNA sequencing analysis of 22 tissues using long-read sequencing and identified 232 novel non-RefSeq isoforms. Collectively, our comprehensive transcriptomic analysis can serve as an important resource for the biological and functional interpretation of gene expression and enable the mechanistic interpretation of genetic disorders and economic traits in Japanese Black cattle.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/02/c1/dsac032.PMC9555877.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40334015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana. 染色体水平和图形基因组提供了对蒙大拿葛根生物活性代谢物代谢和冷适应的见解。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-08-23 DOI: 10.1093/dnares/dsac030

Changjuan Mo, Zhengdan Wu, Xiaohong Shang, Pingli Shi, Minghua Wei, Haiyan Wang, Liang Xiao, Sheng Cao, Liuying Lu, Wendan Zeng, Huabing Yan, Qiusheng Kong

{"title":"Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana.","authors":"Changjuan Mo, Zhengdan Wu, Xiaohong Shang, Pingli Shi, Minghua Wei, Haiyan Wang, Liang Xiao, Sheng Cao, Liuying Lu, Wendan Zeng, Huabing Yan, Qiusheng Kong","doi":"10.1093/dnares/dsac030","DOIUrl":"https://doi.org/10.1093/dnares/dsac030","url":null,"abstract":"Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f7/7f/dsac030.PMC9397507.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40607255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5