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Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. Xyrichtys novacula(林奈,1758)基因组的染色体水平组装和注释。
IF 3.9 2区 生物学
DNA Research Pub Date : 2023-10-01 DOI: 10.1093/dnares/dsad021
Fernando Cruz, Jèssica Gómez-Garrido, Marta Gut, Tyler S Alioto, Joan Pons, Josep Alós, Margarida Barcelo-Serra
{"title":"Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome.","authors":"Fernando Cruz, Jèssica Gómez-Garrido, Marta Gut, Tyler S Alioto, Joan Pons, Josep Alós, Margarida Barcelo-Serra","doi":"10.1093/dnares/dsad021","DOIUrl":"10.1093/dnares/dsad021","url":null,"abstract":"<p><p>The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness > 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10590160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41150703","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
Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes. 通过对四个基因组的分析,揭示炭形目牙齿个体发生的基因组特征、系统发育和遗传基础。
IF 3.9 2区 生物学
DNA Research Pub Date : 2023-10-01 DOI: 10.1093/dnares/dsad022
Xianwei Yang, Yue Song, Rui Zhang, Mengjun Yu, Xinyu Guo, Haobing Guo, Xiao Du, Shuai Sun, Chunhua Li, Xuebin Mao, Guangyi Fan, Xin Liu
{"title":"Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes.","authors":"Xianwei Yang, Yue Song, Rui Zhang, Mengjun Yu, Xinyu Guo, Haobing Guo, Xiao Du, Shuai Sun, Chunhua Li, Xuebin Mao, Guangyi Fan, Xin Liu","doi":"10.1093/dnares/dsad022","DOIUrl":"10.1093/dnares/dsad022","url":null,"abstract":"<p><p>Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10590162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41162960","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 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。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-10-01 DOI: 10.1093/dnares/dsad019
Shizuka Koshimizu, Sachiko Masuda, Arisa Shibata, Takayoshi Ishii, Ken Shirasu, Atsushi Hoshino, Masanori Arita
{"title":"Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.","authors":"Shizuka Koshimizu,&nbsp;Sachiko Masuda,&nbsp;Arisa Shibata,&nbsp;Takayoshi Ishii,&nbsp;Ken Shirasu,&nbsp;Atsushi Hoshino,&nbsp;Masanori Arita","doi":"10.1093/dnares/dsad019","DOIUrl":"10.1093/dnares/dsad019","url":null,"abstract":"<p><p>Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10558197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10554328","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 pioneer species Plantago major L. (Plantaginaceae) provides insight into its global distribution and adaptation to metal-contaminated soil. 车前草(Plantago major L.,车前草科)的基因组组装有助于了解其全球分布及其对金属污染土壤的适应。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad013
Shanwu Lyu, Qiming Mei, Hui Liu, Baosheng Wang, Jun Wang, Hans Lambers, Zhengfeng Wang, Bin Dong, Zhanfeng Liu, Shulin Deng
{"title":"Genome assembly of the pioneer species Plantago major L. (Plantaginaceae) provides insight into its global distribution and adaptation to metal-contaminated soil.","authors":"Shanwu Lyu,&nbsp;Qiming Mei,&nbsp;Hui Liu,&nbsp;Baosheng Wang,&nbsp;Jun Wang,&nbsp;Hans Lambers,&nbsp;Zhengfeng Wang,&nbsp;Bin Dong,&nbsp;Zhanfeng Liu,&nbsp;Shulin Deng","doi":"10.1093/dnares/dsad013","DOIUrl":"https://doi.org/10.1093/dnares/dsad013","url":null,"abstract":"<p><p>Plantago is a major genus belonging to the Plantaginaceae family and is used in herbal medicine, functional food, and pastures. Several Plantago species are also characterized by their global distribution, but the mechanism underpinning this is not known. Here, we present a high-quality, chromosome-level genome assembly of Plantago major L., a species of Plantago, by incorporating Oxford Nanopore sequencing and Hi-C technologies. The genome assembly size was approximately 671.27 Mb with a contig N50 length of 31.30 Mb. 31,654 protein-coding genes were identified from the genome. Evolutionary analysis showed that P. major diverged from other Lamiales species at ~62.18 Mya and experienced two rounds of WGD events. Notably, many gene families related to plant acclimation and adaptation expanded. We also found that many polyphenol biosynthesis genes showed high expression patterns in roots. Some amino acid biosynthesis genes, such as those involved in histidine synthesis, were highly induced under metal (Ni) stress that led to the accumulation of corresponding metabolites. These results suggest persuasive arguments for the global distribution of P. major through multiscale analysis. Decoding the P. major genome provides a valuable genomic resource for research on dissecting biological function, molecular evolution, taxonomy, and breeding.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10254747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9651551","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
Base-excision restriction enzymes: expanding the world of epigenetic immune systems. 碱基切除限制性内切酶:扩展表观遗传免疫系统的世界。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad009
Kenji K Kojima, Ichizo Kobayashi
{"title":"Base-excision restriction enzymes: expanding the world of epigenetic immune systems.","authors":"Kenji K Kojima,&nbsp;Ichizo Kobayashi","doi":"10.1093/dnares/dsad009","DOIUrl":"https://doi.org/10.1093/dnares/dsad009","url":null,"abstract":"<p><p>The restriction enzymes examined so far are phosphodiesterases, which cleave DNA strands by hydrolysing phosphodiester bonds. Based on the mobility of restriction-modification systems, recent studies have identified a family of restriction enzymes that excise a base in their recognition sequence to generate an abasic (AP) site unless the base is properly methylated. These restriction glycosylases also show intrinsic but uncoupled AP lyase activity at the AP site, generating an atypical strand break. Action of an AP endonuclease at the AP site may generate another atypical break, rejoining/repairing of which is difficult. This PabI family of restriction enzymes contain a novel fold (HALFPIPE) and show unusual properties, such as non-requirement of divalent cations for cleavage. These enzymes are present in Helicobacteraceae/Campylobacteraceae and in few hyperthermophilic archaeal species. In Helicobacter genomes, their recognition sites are strongly avoided, and the encoding genes are often inactivated by mutations or replacement, indicating that their expression is toxic for the cells. The discovery of restriction glycosylases generalizes the concept of restriction-modification systems to epigenetic immune systems, which may use any mode of damage to DNA that are considered 'non-self' based on epigenetic modifications. This concept will add to our understanding of immunity and epigenetics.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10273834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9654022","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 and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma. 基因组学和转录组学分析阐明了一种管虫独特生活方式的分子基础。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad014
Taiga Uchida, Yuki Yoshioka, Yu Yoshida, Manabu Fujie, Ayuta Yamaki, Akira Sasaki, Koji Inoue, Chuya Shinzato
{"title":"Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma.","authors":"Taiga Uchida,&nbsp;Yuki Yoshioka,&nbsp;Yu Yoshida,&nbsp;Manabu Fujie,&nbsp;Ayuta Yamaki,&nbsp;Akira Sasaki,&nbsp;Koji Inoue,&nbsp;Chuya Shinzato","doi":"10.1093/dnares/dsad014","DOIUrl":"https://doi.org/10.1093/dnares/dsad014","url":null,"abstract":"<p><p>Vestimentiferan tubeworms are representative members of deep-sea chemosynthetic ecosystems. In this study, we developed a draft genome and gene models and performed genomic and transcriptomic analyses of Lamellibrachia satsuma, the only vestimentiferan reported from the euphotic zone. The quality of the genome assembly and gene models is comparable to or higher than those of previously reported vestimentiferan tubeworms. Tissue-specific transcriptome sequencing revealed that Toll-like receptor genes and lineage-specific expanded bacteriolytic enzyme genes are highly expressed in the obturacular and vestimental regions, respectively, suggesting the importance of these tissues in defense against pathogens. On the other hand, globin subunit genes are expressed almost exclusively in the trunk region, supporting the hypothesis that the trophosome is the site of haemoglobin biosynthesis. Vestimentiferan-specific expanded gene families included chitinases, ion channels, and C-type lectins, suggesting the importance of these functions for vestimentiferans. C-type lectins in the trunk region, in particular, may be involved in recognition of pathogens, or in interactions between tubeworms and symbiotic bacteria. Our genomic and transcriptomic analyses enhance understanding of molecular mechanisms underlying the unique lifestyle of vestimentiferan tubeworms, particularly their obligate mutualism with chemosynthetic bacteria.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b0/c3/dsad014.PMC10291997.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10072083","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
GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level. GINGER:在基因和外显子水平高精度预测高等真核生物基因结构的综合方法。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad017
Takeaki Taniguchi, Miki Okuno, Takahiro Shinoda, Fumiya Kobayashi, Kazuki Takahashi, Hideaki Yuasa, Yuta Nakamura, Hiroyuki Tanaka, Rei Kajitani, Takehiko Itoh
{"title":"GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level.","authors":"Takeaki Taniguchi, Miki Okuno, Takahiro Shinoda, Fumiya Kobayashi, Kazuki Takahashi, Hideaki Yuasa, Yuta Nakamura, Hiroyuki Tanaka, Rei Kajitani, Takehiko Itoh","doi":"10.1093/dnares/dsad017","DOIUrl":"10.1093/dnares/dsad017","url":null,"abstract":"<p><p>The prediction of gene structure within the genome sequence is the starting point of genome analysis, and its accuracy has a significant impact on the quality of subsequent analyses. Gene structure prediction is roughly divided into RNA-Seq-based methods, ab initio-based methods, homology-based methods, and the integration of individual prediction methods. Integrated methods are mainstream in recent genome projects because they improve prediction accuracy by combining or taking the best individual prediction findings; however, adequate prediction accuracy for eukaryotic species has not yet been achieved. Therefore, we developed an integrated tool, GINGER, that solves various issues related to gene structure prediction in higher eukaryotes. By handling artefacts in alignments of RNA and protein sequences, reconstructing gene structures via dynamic programming with appropriately weighted and scored exon/intron/intergenic regions, and applying different prediction processes and filtering criteria to multi-exon and single-exon genes, we achieved a significant improvement in accuracy compared to the existing integration methods. The feature of GINGER is its high prediction accuracy at the gene and exon levels, which is pronounced for species with more complex gene architectures. GINGER is implemented using Nextflow, which allows for the efficient and effective use of computing resources.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cb/45/dsad017.PMC10439787.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10042560","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 an endangered plant Prunus mongolica using PacBio and Hi-C technologies. 利用PacBio和Hi-C技术对濒危植物蒙古李染色体水平基因组进行组装。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad012
Qiang Zhu, Yali Wang, Ning Yao, Xilu Ni, Cuiping Wang, Meng Wang, Lei Zhang, Wenyu Liang
{"title":"Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies.","authors":"Qiang Zhu,&nbsp;Yali Wang,&nbsp;Ning Yao,&nbsp;Xilu Ni,&nbsp;Cuiping Wang,&nbsp;Meng Wang,&nbsp;Lei Zhang,&nbsp;Wenyu Liang","doi":"10.1093/dnares/dsad012","DOIUrl":"https://doi.org/10.1093/dnares/dsad012","url":null,"abstract":"<p><p>Prunus mongolica is an ecologically and economically important xerophytic tree native to Northwest China. Here, we report a high-quality, chromosome-level P. mongolica genome assembly integrating PacBio high-fidelity sequencing and Hi-C technology. The assembled genome was 233.17 Mb in size, with 98.89% assigned to eight pseudochromosomes. The genome had contig and scaffold N50s of 24.33 Mb and 26.54 Mb, respectively, a BUSCO completeness score of 98.76%, and CEGMA indicated that 98.47% of the assembled genome was reliably annotated. The genome contained a total of 88.54 Mb (37.97%) of repetitive sequences and 23,798 protein-coding genes. We found that P. mongolica experienced two whole-genome duplications, with the most recent event occurring ~3.57 million years ago. Phylogenetic and chromosome syntenic analyses revealed that P. mongolica was closely related to P. persica and P. dulcis. Furthermore, we identified a number of candidate genes involved in drought tolerance and fatty acid biosynthesis. These candidate genes are likely to prove useful in studies of drought tolerance and fatty acid biosynthesis in P. mongolica, and will provide important genetic resources for molecular breeding and improvement experiments in Prunus species. This high-quality reference genome will also accelerate the study of the adaptation of xerophytic plants to drought.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10254739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9652478","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
Self-grafting-induced epigenetic changes leading to drought stress tolerance in tomato plants. 番茄植株自嫁接诱导的抗干旱表观遗传变化。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-08-01 DOI: 10.1093/dnares/dsad016
Maria Isabel Fuentes-Merlos, Masaru Bamba, Shusei Sato, Atsushi Higashitani
{"title":"Self-grafting-induced epigenetic changes leading to drought stress tolerance in tomato plants.","authors":"Maria Isabel Fuentes-Merlos,&nbsp;Masaru Bamba,&nbsp;Shusei Sato,&nbsp;Atsushi Higashitani","doi":"10.1093/dnares/dsad016","DOIUrl":"https://doi.org/10.1093/dnares/dsad016","url":null,"abstract":"<p><p>Grafting is widely used as a method to increase stress tolerance in good fruiting lines of Solanaceae plants. However, little is known about how grafting, affects epigenetic modifications and leads to stress tolerance, especially within the same line. Here, we studied the effects of self-grafting in tomato plants on histone and DNA modifications and changes in gene expression related to drought stress. We found that at the three-leaf stage, 1 week after self-grafting, histone H3 K4 trimethylation and K27 trimethylation changes were observed in more than 500 genes each, and DNA methylation changes in more than 5,000 gene regions at the shoot apex compared to the non-grafted control. In addition, two weeks after the epigenomic changes, global expression changes continued to be observed at the shoot apex in several genes related to the metabolic process of nitrogen compounds, responses to stimulus, chromosome organization, cell cycle-related genes, and regulation of hormone levels. Finally, these grafted seedlings acquired remarkable drought tolerance, suggesting that epigenomic modifications during the wound-healing process mitigate stress tolerance in tomato plants.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10368339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9877002","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
Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community. 使用新构建的人类肠道微生物组模拟群落评估宏基因组工作流程。
IF 4.1 2区 生物学
DNA Research Pub Date : 2023-06-01 DOI: 10.1093/dnares/dsad010
Hiroshi Mori, Tamotsu Kato, Hiroaki Ozawa, Mitsuo Sakamoto, Takumi Murakami, Todd D Taylor, Atsushi Toyoda, Moriya Ohkuma, Ken Kurokawa, Hiroshi Ohno
{"title":"Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.","authors":"Hiroshi Mori,&nbsp;Tamotsu Kato,&nbsp;Hiroaki Ozawa,&nbsp;Mitsuo Sakamoto,&nbsp;Takumi Murakami,&nbsp;Todd D Taylor,&nbsp;Atsushi Toyoda,&nbsp;Moriya Ohkuma,&nbsp;Ken Kurokawa,&nbsp;Hiroshi Ohno","doi":"10.1093/dnares/dsad010","DOIUrl":"https://doi.org/10.1093/dnares/dsad010","url":null,"abstract":"<p><p>To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 3","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10229288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9916361","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
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