DNA Research最新文献_第2页

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. 高完整性葛根变种叶基因组和种群分析揭示了葛根属的遗传多样性。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae017

Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan

{"title":"High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.","authors":"Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan","doi":"10.1093/dnares/dsae017","DOIUrl":"10.1093/dnares/dsae017","url":null,"abstract":"Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176847","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

Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea. 揭示 DNA 甲基化景观，解读鹰嘴豆表型多样性的进化足迹。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae013

Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida

{"title":"Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.","authors":"Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida","doi":"10.1093/dnares/dsae013","DOIUrl":"10.1093/dnares/dsae013","url":null,"abstract":"Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874953","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

Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq. 利用 PacBio Iso-Seq 和 RNA-Seq 分析梅氏海鯈鱼盐碱胁迫适应过程中转录组变化的特征。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae019

Dan Yu, Min Zhou, Wenjun Chen, Zufa Ding, Cheng Wang, Yuting Qian, Yang Liu, Shunping He, Liandong Yang

{"title":"Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq.","authors":"Dan Yu, Min Zhou, Wenjun Chen, Zufa Ding, Cheng Wang, Yuting Qian, Yang Liu, Shunping He, Liandong Yang","doi":"10.1093/dnares/dsae019","DOIUrl":"10.1093/dnares/dsae019","url":null,"abstract":"Leuciscus merzbacheri is a native fish species found exclusively in the Junggar Basin in Xinjiang. It exhibits remarkable adaptability, thriving in varying water conditions such as the saline waters, the semi-saline water, and the freshwater. Despite its significant economic and ecological value, the underlying mechanisms of its remarkable salinity tolerance remain elusive. Our study marks the first time the full-length transcriptome of L. merzbacheri has been reported, utilizing RNA-Seq and PacBio Iso-Seq technologies. We found that the average length of the full-length transcriptome is 1,780 bp, with an N50 length of 2,358 bp. We collected RNA-Seq data from gill, liver, and kidney tissues of L. merzbacheri from both saline water and freshwater environments and conducted comparative analyses across these tissues. Further analysis revealed significant enrichment in several key functional gene categories and signalling pathways related to stress response and environmental adaptation. The findings provide a valuable genetic resource for further investigation into saline-responsive candidate genes, which will deepen our understanding of teleost adaptation to extreme environmental stress. This knowledge is crucial for the future breeding and conservation of native fish species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11161863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162695","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

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis. 北太平洋海星 Asterias amurensis 的高质量染色体级基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae007

Zhichao Huang, Qi Liu, Xiaoqi Zeng, Gang Ni

{"title":"High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis.","authors":"Zhichao Huang, Qi Liu, Xiaoqi Zeng, Gang Ni","doi":"10.1093/dnares/dsae007","DOIUrl":"10.1093/dnares/dsae007","url":null,"abstract":"Asterias amurensis, a starfish species that is native to countries such as China and Japan, as well as non-native regions like Australia, has raised serious concerns in terms of its impact on ecology and economy. To gain a better understanding of its population genomics and dynamics, we successfully assembled a high-quality chromosome-level genome of A. amurensis using PacBio and Hi-C sequencing technologies. A total of 87 scaffolds assembly with contig N50 length of 10.85 Mb and scaffold N50 length of 23.34 Mb were obtained, with over 98.80% (0.48 Gb) of them anchored to 22 pseudochromosomes. We predicted 16,673 protein-coding genes, 95.19% of which were functionally annotated. Our phylogenetic analysis revealed that A. amurensis and Asterias rubens formed a clade, and their divergence time was estimated ~ 28 million years ago (Mya). The significantly enriched pathways and Gene Ontology terms related to the amplified gene family were mainly associated with immune response and energy metabolism, suggesting that these factors might have contributed to the adaptability of A. amurensis to its environment. This study provides valuable genomic resources for comprehending the genetics, dynamics, and evolution of A. amurensis, especially when population outbreaks or invasions occur.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984453","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 Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal. 元氏萤火虫（Nipponoluciola cruciata）基因组组装揭示了新型荧光素酶样发光蛋白，但没有过氧化物酶体靶向信号。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae006

Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi

{"title":"Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal.","authors":"Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi","doi":"10.1093/dnares/dsae006","DOIUrl":"10.1093/dnares/dsae006","url":null,"abstract":"The Genji firefly, Nipponoluciola cruciata, is an aquatic firefly endemic to Japan, inhabiting a wide area of the Japanese archipelago. The luminescence of fireflies is a scientifically interesting phenomenon, and many studies have evaluated this species in Japan. In this study, we sequenced the whole genome of male N. cruciata and constructed a high-quality genome assembly of 662 Mb with a BUSCO completeness of 99.1% in the genome mode. Using the detected set of 15,169 protein-coding genes, the genomic structures and genetic background of luminescence-related genes were also investigated. We found four new firefly luciferase-like genes in the genome. The highest bioluminescent activity was observed for LLa2, which originated from ancestral PDGY, a mitochondrial acyl-CoA synthetase. A thioesterase candidate, NcruACOT1, which is involved in d-luciferin biosynthesis, was expressed in the lantern. Two opsins were also detected and the absorption wavelength of the UV-type opsin candidate shifted from UV to blue. These findings provide an important resource for unravelling the adaptive evolution of fireflies in terms of luminescence and vision.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"31 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144533","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

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. 太平洋秋刀鱼基因组的染色体 DNA 序列：渔业科学和比较生物学的多功能资源。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae004

Mana Sato, Kazuya Fukuda, Mitsutaka Kadota, Hatsune Makino-Itou, Kaori Tatsumi, Shinya Yamauchi, Shigehiro Kuraku

{"title":"Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.","authors":"Mana Sato, Kazuya Fukuda, Mitsutaka Kadota, Hatsune Makino-Itou, Kaori Tatsumi, Shinya Yamauchi, Shigehiro Kuraku","doi":"10.1093/dnares/dsae004","DOIUrl":"10.1093/dnares/dsae004","url":null,"abstract":"Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"31 2","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061158","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

Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. 基于转座子介导的猪基因组多态性的种群遗传分析。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae008

Wencheng Zong, Runze Zhao, Xiaoyan Wang, Chenyu Zhou, Jinbu Wang, Cai Chen, Naiqi Niu, Yao Zheng, Li Chen, Xin Liu, Xinhua Hou, Fuping Zhao, Ligang Wang, Lixian Wang, Chengyi Song, Longchao Zhang

{"title":"Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig.","authors":"Wencheng Zong, Runze Zhao, Xiaoyan Wang, Chenyu Zhou, Jinbu Wang, Cai Chen, Naiqi Niu, Yao Zheng, Li Chen, Xin Liu, Xinhua Hou, Fuping Zhao, Ligang Wang, Lixian Wang, Chengyi Song, Longchao Zhang","doi":"10.1093/dnares/dsae008","DOIUrl":"10.1093/dnares/dsae008","url":null,"abstract":"Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050934","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

Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection. 评估全球野生大豆（Glycine soja Sieb. et Zucc.）

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae009

Feng Li, Takashi Sayama, Yuko Yokota, Susumu Hiraga, Masatsugu Hashiguchi, Hidenori Tanaka, Ryo Akashi, Masao Ishimoto

{"title":"Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.","authors":"Feng Li, Takashi Sayama, Yuko Yokota, Susumu Hiraga, Masatsugu Hashiguchi, Hidenori Tanaka, Ryo Akashi, Masao Ishimoto","doi":"10.1093/dnares/dsae009","DOIUrl":"10.1093/dnares/dsae009","url":null,"abstract":"Wild soybean (Glycine soja), the ancestor of the cultivated soybean (G. max), is a crucial resource for capturing the genetic diversity of soybean species. In this study, we used a set of 78 genome-wide microsatellite markers to analyse the genetic diversity and geographic differentiation patterns in a global collection of 2,050 G. soja accessions and a mini-core collection of G. max stored in two public seed banks. We observed a notable reduction in the genetic diversity of G. max compared with G. soja and identified a close phylogenetic relationship between G. max and a G. soja subpopulation located in central China. Furthermore, we revealed substantial genetic divergence between northern and southern subpopulations, accompanied by diminished genetic diversity in the northern subpopulations. Two clusters were discovered among the accessions from north-eastern China-one genetically close to those from South Korea and Southern Japan, and another close to those from Amur Oblast, Russia. Finally, 192 accessions were assigned to a mini-core collection of G. soja, retaining 73.8% of the alleles detected in the entire collection. This mini-core collection is accessible to those who need it, facilitating efficient evaluation and utilization of G. soja genetic resources in soybean breeding initiatives.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae. 沉水植物 Cryptocoryne crispatula 染色体水平的基因组为了解天南星科陆地-淡水过渡提供了线索。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-02-01 DOI: 10.1093/dnares/dsae003

Zhi-Hao Qian, Wei Li, Qing-Feng Wang, Shi-Chu Liang, Shuang Wu, Zhi-Zhong Li, Jin-Ming Chen

{"title":"The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae.","authors":"Zhi-Hao Qian, Wei Li, Qing-Feng Wang, Shi-Chu Liang, Shuang Wu, Zhi-Zhong Li, Jin-Ming Chen","doi":"10.1093/dnares/dsae003","DOIUrl":"10.1093/dnares/dsae003","url":null,"abstract":"Plant terrestrialization (i.e. the transition to a terrestrial environment) is a significant evolutionary event that has been intensively studied. While certain plant lineages, particularly in angiosperms, have re-adapted to freshwater habitats after colonizing terrene, however, the molecular mechanism of the terrestrial-freshwater (T-F) transition remains limited. Here, the basal monocot Araceae was selected as the study object to explore the T-F transition adaptation mechanism by comparative genomic analysis. Our findings revealed that the substitution rates significantly increased in the lineage of freshwater Araceae, which may promote their adaptation to the freshwater habitat. Additionally, 20 gene sets across all four freshwater species displayed signs of positive selection contributing to tissue development and defense responses in freshwater plants. Comparative synteny analysis showed that genes specific to submerged plants were enriched in cellular respiration and photosynthesis. In contrast, floating plants were involved in regulating gene expression, suggesting that gene and genome duplications may provide the original material for plants to adapt to the freshwater environment. Our study provides valuable insights into the genomic aspects of the transition from terrestrial to aquatic environments in Araceae, laying the groundwork for future research in the angiosperm.","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/PMC10873505/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139514188","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

A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis. 通过系统缺失分析，确定了质粒 Rts1 高效连接所需的全部基因列表。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-02-01 DOI: 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":"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.","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}

引用次数: 0