DNA ResearchPub Date : 2024-02-01DOI: 10.1093/dnares/dsae002
Takahiro Murata, Yasuhiro Gotoh, Tetsuya Hayashi
{"title":"A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis.","authors":"Takahiro Murata, Yasuhiro Gotoh, Tetsuya Hayashi","doi":"10.1093/dnares/dsae002","DOIUrl":"10.1093/dnares/dsae002","url":null,"abstract":"<p><p>While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652123","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}
DNA ResearchPub Date : 2024-02-01DOI: 10.1093/dnares/dsad028
Zheng-Feng Wang, Lin Fu, En-Ping Yu, Wei-Guang Zhu, Song-Jun Zeng, Hong-Lin Cao
{"title":"Chromosome-level genome assembly and demographic history of Euryodendron excelsum in monotypic genus endemic to China.","authors":"Zheng-Feng Wang, Lin Fu, En-Ping Yu, Wei-Guang Zhu, Song-Jun Zeng, Hong-Lin Cao","doi":"10.1093/dnares/dsad028","DOIUrl":"10.1093/dnares/dsad028","url":null,"abstract":"<p><p>Euryodendron excelsum is in a monotypic genus Euryodendron, endemic to China. It has intermediate morphisms in the Pentaphylacaceae or Theaceae families, which make it distinct. Due to anthropogenic disturbance, E. excelsum is currently found in very restricted and fragmented areas with extremely small populations. Although much research and effort has been applied towards its conservation, its long-term survival mechanisms and evolutionary history remain elusive, especially from a genomic aspect. Therefore, using a combination of long/short whole genome sequencing, RNA sequencing reads, and Hi-C data, we assembled and annotated a high-quality genome for E. excelsum. The genome assembly of E. excelsum comprised 1,059,895,887 bp with 99.66% anchored into 23 pseudo-chromosomes and a 99.0% BUSCO completeness. Comparative genomic analysis revealed the expansion of terpenoid and flavonoid secondary metabolite genes, and displayed a tandem and/or proximal duplication framework of these genes. E. excelsum also displayed genes associated with growth, development, and defence adaptation from whole genome duplication. Demographic analysis indicated that its fluctuations in population size and its recent population decline were related to cold climate changes. The E. excelsum genome assembly provides a highly valuable resource for evolutionary and ecological research in the future, aiding its conservation, management, and restoration.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10781514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040875","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}
DNA ResearchPub Date : 2024-02-01DOI: 10.1093/dnares/dsad026
Jiankang Wang, Ryuichiro Nakato
{"title":"Churros: a Docker-based pipeline for large-scale epigenomic analysis.","authors":"Jiankang Wang, Ryuichiro Nakato","doi":"10.1093/dnares/dsad026","DOIUrl":"10.1093/dnares/dsad026","url":null,"abstract":"<p><p>The epigenome, which reflects the modifications on chromatin or DNA sequences, provides crucial insight into gene expression regulation and cellular activity. With the continuous accumulation of epigenomic datasets such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) data, there is a great demand for a streamlined pipeline to consistently process them, especially for large-dataset comparisons involving hundreds of samples. Here, we present Churros, an end-to-end epigenomic analysis pipeline that is environmentally independent and optimized for handling large-scale data. We successfully demonstrated the effectiveness of Churros by analyzing large-scale ChIP-seq datasets with the hg38 or Telomere-to-Telomere (T2T) human reference genome. We found that applying T2T to the typical analysis workflow has important impacts on read mapping, quality checks, and peak calling. We also introduced a useful feature to study context-specific epigenomic landscapes. Churros will contribute a comprehensive and unified resource for analyzing large-scale epigenomic data.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11389749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138800485","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}
DNA ResearchPub Date : 2024-01-01DOI: 10.1093/dnares/dsae005
Katarina C Stuart, Rebecca N Johnson, Richard E Major, Kamolphat Atsawawaranunt, Kyle M Ewart, Lee A Rollins, Anna W Santure, Annabel Whibley
{"title":"The genome of a globally invasive passerine, the common myna, Acridotheres tristis.","authors":"Katarina C Stuart, Rebecca N Johnson, Richard E Major, Kamolphat Atsawawaranunt, Kyle M Ewart, Lee A Rollins, Anna W Santure, Annabel Whibley","doi":"10.1093/dnares/dsae005","DOIUrl":"10.1093/dnares/dsae005","url":null,"abstract":"<p><p>In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747746","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}
DNA ResearchPub Date : 2023-12-01DOI: 10.1093/dnares/dsad025
Amanda Christine Ramdass, Sephra Nalini Rampersad
{"title":"Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains.","authors":"Amanda Christine Ramdass, Sephra Nalini Rampersad","doi":"10.1093/dnares/dsad025","DOIUrl":"10.1093/dnares/dsad025","url":null,"abstract":"<p><p>For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10710014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720459","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}
{"title":"Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan.","authors":"Yukie Kashima, Taketoshi Mizutani, Yuki Okimoto, Minami Maeda, Kaoru Musashino, Ryo-Ichi Nishide, Akira Matsukura, Jison Nagase, Yutaka Suzuki","doi":"10.1093/dnares/dsad020","DOIUrl":"10.1093/dnares/dsad020","url":null,"abstract":"<p><p>Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spread of SARS-CoV-2 and its evolutionary convergence in Kashiwa City, as an example of a representative commuter town in Japan. From September 2020 to January 2023, a total of 47,134 nasopharyngeal swab and saliva specimens were collected from patients in 47 local clinics and hospitals, covering the vast majority of healthcare facilities. All SARS-CoV-2-positive samples were subjected to whole genome sequencing. Based on the analysis of 5,536 identified genomes, all major strains were represented. Unique regional mutations were occasionally identified in each strain. Inspection of these mutations revealed that the overall base substitution rate increased with progressive waves of the pandemic, at an overall rate of 2.56 bases/year. Interestingly, the spread and evolutionary patterns appeared to be distinct between regions and between individual clinics. Further analysis of the synonymous base substitution rate showed that the speed of viral evolution accelerated coincident with the beginning of public vaccination. Comprehensive genomic epidemiological studies, as presented here, should be useful in precisely understanding the pandemic and preparing for possible future pandemics.</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://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8b/70/dsad020.PMC10562954.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10592178","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}
DNA ResearchPub Date : 2023-10-01DOI: 10.1093/dnares/dsad023
Mitsuhiko P Sato, Satoshi Iwakami, Kanade Fukunishi, Kai Sugiura, Kentaro Yasuda, Sachiko Isobe, Kenta Shirasawa
{"title":"Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.","authors":"Mitsuhiko P Sato, Satoshi Iwakami, Kanade Fukunishi, Kai Sugiura, Kentaro Yasuda, Sachiko Isobe, Kenta Shirasawa","doi":"10.1093/dnares/dsad023","DOIUrl":"10.1093/dnares/dsad023","url":null,"abstract":"<p><p>Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 5","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523329","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}
{"title":"Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon.","authors":"Ayano Horiuchi, Kanae Masuda, Kenta Shirasawa, Noriyuki Onoue, Ryusuke Matsuzaki, Ryutaro Tao, Yasutaka Kubo, Koichiro Ushijima, Takashi Akagi","doi":"10.1093/dnares/dsad015","DOIUrl":"10.1093/dnares/dsad015","url":null,"abstract":"<p><p>Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties in applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characteristics, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"30 5","pages":""},"PeriodicalIF":4.1,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5c/6e/dsad015.PMC10468310.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10489365","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}
DNA ResearchPub Date : 2023-10-01DOI: 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}
{"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}