DNA Research最新文献

Integrative Transcriptomic Analysis Reveals Alternative Splicing Complexity and Transcriptomic Diversity in Porcine Placentas Across Altitudes. 整合转录组学分析揭示了不同海拔地区猪胎盘剪接复杂性和转录组学多样性。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-05-30 DOI: 10.1093/dnares/dsaf008

Chang-Yao Li, Xin-Tong Meng, Zhi-Peng Liu, Xia Zhang, Biao Zhou, Pubuzhaxi, Hong-Yang Zhao, Jia-Ding Zhao, Guo-Wen Fu, Yong-Cheng Chang, Shao-Rong Gong, Jin-Long Huo, Gui-Ying Zhao

{"title":"Integrative Transcriptomic Analysis Reveals Alternative Splicing Complexity and Transcriptomic Diversity in Porcine Placentas Across Altitudes.","authors":"Chang-Yao Li, Xin-Tong Meng, Zhi-Peng Liu, Xia Zhang, Biao Zhou, Pubuzhaxi, Hong-Yang Zhao, Jia-Ding Zhao, Guo-Wen Fu, Yong-Cheng Chang, Shao-Rong Gong, Jin-Long Huo, Gui-Ying Zhao","doi":"10.1093/dnares/dsaf008","DOIUrl":"https://doi.org/10.1093/dnares/dsaf008","url":null,"abstract":"High-altitude hypoxia provides a natural laboratory for studying adaptation in plateau mammals. As an interface for oxygen and nutrient exchange, placenta plays a critical role in fetal development. While high-altitude adaptation in systemic physiological responses and cardiopulmonary tissues has been well-studied, a comprehensive landscape of porcine placental transcriptomic diversity and alternative splicing (AS) complexity across altitudes remains lacking. Here, we integrated Iso-Seq and RNA-Seq to profile placental transcriptomes from placentas of three pig breeds across altitudes: the Diannan small-ear pig (DSE ~500m), the Baoshan pig (BS ~1500m), and the Changdu Tibetan Pig (CT ~3500m). We identified 39,776 full-length transcripts, including 25,471 novel ones, significantly enhancing pig genome annotation. Additionally, 24,879 AS events from 8,390 AS genes were detected, with skipping exon (SE) as the most prevalent AS type. Differential expression (DE) and differential alternative splicing (DAS) analyses highlighted key DEGs (IGF1, GHR, RASGRP4, MECOM, SPP1), as well as DAS genes (HIF1A, HSPA8, RHOA, HMGCR, PLAGL1), which may be implicated in placental adaptation to high-altitude conditions. This study provides a comprehensive analysis of the transcriptomic diversity and AS complexity in porcine placentas across altitudes, laying a foundation for future investigations into the molecular mechanisms underlying high-altitude adaptation in plateau mammals.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop. 番荔枝高质量基因组组装为新兴水果作物提供功能见解。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-05-28 DOI: 10.1093/dnares/dsaf007

Manohar S Bisht, Shruti Mahajan, Abhisek Chakraborty, Vineet K Sharma

{"title":"A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop.","authors":"Manohar S Bisht, Shruti Mahajan, Abhisek Chakraborty, Vineet K Sharma","doi":"10.1093/dnares/dsaf007","DOIUrl":"10.1093/dnares/dsaf007","url":null,"abstract":"Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution, and demographic history. The genome has a size of 730.4 Mb with an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots. Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole-genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation, and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptive evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value, and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12116420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081936","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

Whole-genome sequencing of the ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae). 蚁群的全基因组测序（膜翅目：蚁科：蚁科）。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-05-20 DOI: 10.1093/dnares/dsaf012

Ayako Gotoh, Atsushi Toyoda, Takahiro Yamabe, Takehiko Itoh

引用次数: 0

Comparative genomics of Endophytic Fungi Apiospora malaysiana with related Ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity. 马来西亚内生真菌Apiospora malaysiana与相关子囊菌的比较基因组学表明，适应生活方式的选择具有潜在的可持续纤维素分解活性。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-05-10 DOI: 10.1093/dnares/dsaf011

Shashi Kant, Sreyashi Das, Subhajeet Dutta, Kajal Mandal, Aditya Upadhyay, Aditya N Sarangi, Rajib Majumder, Sucheta Tripathy

{"title":"Comparative genomics of Endophytic Fungi Apiospora malaysiana with related Ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.","authors":"Shashi Kant, Sreyashi Das, Subhajeet Dutta, Kajal Mandal, Aditya Upadhyay, Aditya N Sarangi, Rajib Majumder, Sucheta Tripathy","doi":"10.1093/dnares/dsaf011","DOIUrl":"https://doi.org/10.1093/dnares/dsaf011","url":null,"abstract":"Ascomycetes fungi produce Carbohydrate-Active enzymes that are prized in the biofuel industry. Comparative genome analysis of endophytic fungus Apiospora malaysiana with seven other closely related high quality genomes of endophytic and pathogenic organisms reveal that effectors and pathogenicity-related genes are predominantly localized within rapidly evolving gene-sparse regions rather than in the conserved region. This suggests bipartite genome architecture where the rapidly evolving region plays a role in host adaptation. Endophytic fungi adapt to plant invasion by enriching enzymes that degrade cellulose, hemicellulose, lignin, and pectin. In contrast, we observed pathogenic fungi, especially N. oryzae, shows a reduced number of secondary metabolites biosysnthesis and catabolism, reflecting lifestyle adaptation. The presence of exclusive sporulating gene clusters in pathogen species could possibly indicate their pathogenic affiliation. Limited genome plasticity and low heterozygosity in A. malaysiana are in line with its predominant asexual life cycle choices in lab conditions. The secretome of A. malaysiana grown in cellulose only media had more cellulase activities when compared to cultures grown in YPD media. Genes that were differentially up-regulated in cellulose-only media exhibited strong cellulose-degrading activity and genes involved in evading detection by hosts surveillance system. Successful cloning and expression of selected CAZymes in bacterial expression systems with desirable physicochemical properties highlight the biotechnological potential of A. malaysiana for sustainable enzyme cellulolytic enzyme production. These findings position endophytes as valuable resources for cellulolytic enzyme research and broader bio-industrial applications.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Four chromosome-scale ampullariid genomes: High-quality resources for ecological, evolutionary and invasion biology studies. 四染色体规模壶体基因组：生态、进化和入侵生物学研究的优质资源。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-05-09 DOI: 10.1093/dnares/dsaf010

Jianxiong Xiong, Yue Gao, Yufei Zhou, Jack Chi-Ho Ip, Santiago Ituarte, Horacio Heras, Jian-Wen Qiu, Jin Sun

{"title":"Four chromosome-scale ampullariid genomes: High-quality resources for ecological, evolutionary and invasion biology studies.","authors":"Jianxiong Xiong, Yue Gao, Yufei Zhou, Jack Chi-Ho Ip, Santiago Ituarte, Horacio Heras, Jian-Wen Qiu, Jin Sun","doi":"10.1093/dnares/dsaf010","DOIUrl":"https://doi.org/10.1093/dnares/dsaf010","url":null,"abstract":"The New World Ampullariids, encompassing the ecologically important genera Pomacea and Marisa, are organisms with dual attributes-serving as model systems for evolutionary and environmental research while posing severe threats as globally invasive species. Here, we present chromosome-scale genomes of four key species-Pomacea canaliculata, P. maculata, P. diffusa, and Marisa cornuarietis-generated through PacBio HiFi sequencing and Hi-C scaffolding. These assemblies exhibit exceptional continuity and completeness (BUSCO scores >95%) with genome sizes ranging 450-540 Mb, while high-quality annotations predicting 21,687-22,481 protein-coding genes per genome. Comparative analysis reveals divergent genome architectures: the invasive P. canaliculata and P. maculata harbour lower LINE (5.7-5.8%) and LTR (0.7-0.8%) content compared to non-invasive P. diffusa (LINE: 7.7%; LTR: 0.8%) and M. cornuarietis (LINE: 9.5%; LTR: 1.1%), suggesting repeat dynamics linked to ecological plasticity. Macrosynteny analyses identify five dynamic but conserved ancestral chromosomal fusions across species but with limited rearrangements among species. These resources, integrating chromosomal resolution with functional annotation, provide a foundation for comparative studies on molluscan karyotype evolution and adaptive radiation research, as well as possible targets for CRISPR-cas9-driven biocontrol strategies.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria. 植物致病性γ变形菌原生质粒的比较基因组学研究。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-04-24 DOI: 10.1093/dnares/dsaf009

Miriam Urriza, Giulio Dimaria, Luiz Orlando de Oliveira, Vittoria Catara, Jesús Murillo

{"title":"Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.","authors":"Miriam Urriza, Giulio Dimaria, Luiz Orlando de Oliveira, Vittoria Catara, Jesús Murillo","doi":"10.1093/dnares/dsaf009","DOIUrl":"https://doi.org/10.1093/dnares/dsaf009","url":null,"abstract":"Plasmids are key in the evolution and adaptation of plant pathogenic Gammaproteobacteria (PPG), yet their diversity and functional contributions remain underexplored. Here, comparative genomics revealed extensive variation in plasmid size, replicon types, mobility, and genetic content across PPG. Most plasmids are small (<200 kb), except in Pantoea, exhibiting high coding densities (76-78%). Five ancestral replicon types were identified across multiple orders, indicating vertical descent yet efficient horizontal transfer across taxa, although with limited genetic conservation. Virulence plasmids are widespread (56-68%) but differ in virulence gene content across orders: type III effector (T3E) genes are common in Pseudomonas and Xanthomonas, but rare in Enterobacterales and Xylella, aligning with their smaller effector repertoires. Plasmids frequently carry regulatory genes, highlighting their role in bacterial phenotype modulation. Distinct patterns were observed among orders: Enterobacterales plasmids often harbor thiamine biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while Pseudomonas and Xanthomonas plasmids are highly mobile, enriched in T3E genes, and exhibit high insertion sequence densities, fostering DNA mobility. Resistance to ultraviolet light is common, but not to antimicrobial compounds. These findings highlight the dynamic role of plasmids in spreading adaptive traits, shaping virulence, and driving the evolution of plant pathogenic bacteria.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours. 马蹄铁（Pontederia cordata L.）染色体水平的基因组组装为其快速适应和花色变异提供了新的思路。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-03-01 DOI: 10.1093/dnares/dsaf002

Jia-Le Wang, Wen-Da Zhang, Xiao-Dong Yang, Pu-Guang Zhao, Xiang-Yu Wang, Shu-Ying Zhao, Ling-Yun Chen

{"title":"Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours.","authors":"Jia-Le Wang, Wen-Da Zhang, Xiao-Dong Yang, Pu-Guang Zhao, Xiang-Yu Wang, Shu-Ying Zhao, Ling-Yun Chen","doi":"10.1093/dnares/dsaf002","DOIUrl":"10.1093/dnares/dsaf002","url":null,"abstract":"Pontederia cordata L. is an aquatic ornamental plant native to the Americas but has been widely distributed in South Asia, Australia, and Europe. The genetic mechanisms behind its rapid adaptation and spread have not yet been well understood. To understand the mechanisms for its rapid adaptation, this study assembled the first chromosome-level genome of P. cordata. The genome assembly, which spans 527.5 Mb, is anchored on 8 pseudochromosomes with a scaffold N50 of 48 Mb and encompasses 29,389 protein-coding genes. Further analyses revealed that P. cordata had experienced 3 whole-genome duplications (WGDs) events. These WGDs are associated with gene family expansion and increased numbers of resistance gene analogs and transcription factors. Positive selection analysis indicated that genes derived from tandem duplication (TD) and proximal duplication were more likely to undergo positive selection, and were enriched in plant defense and disease resistance. These results implied that WGDs, TD, and positive selection enhanced the environmental adaptability of P. cordata. In addition, we found that down-regulation of F3'5'H, DFR, ANS, and UFGT likely caused the flower colour variation for P. cordata from violet to white. The first chromosome-level genome of P. cordata here provides a valuable genomic resource for investigating the rapid adaptation and flower colour variation of the species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061071","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-scale genome assembly of Phyllanthus emblica L. 'Yingyu'. 余甘子染色体尺度基因组组装。“Yingyu”。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-03-01 DOI: 10.1093/dnares/dsaf006

Lumin Zhang, Jianmin Yuan, Tianlei Pu, Wenlin Qu, Xiao Lei, Kaihua Ma, Kunjian Qian, Qiongling Zhao, Chengfei Liao, Jie Jin

{"title":"Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'.","authors":"Lumin Zhang, Jianmin Yuan, Tianlei Pu, Wenlin Qu, Xiao Lei, Kaihua Ma, Kunjian Qian, Qiongling Zhao, Chengfei Liao, Jie Jin","doi":"10.1093/dnares/dsaf006","DOIUrl":"10.1093/dnares/dsaf006","url":null,"abstract":"Phyllanthus emblica L. is an edible plant with medicinal properties native to the dry-hot valley of Yunnan, China. Here, we report a de novo chromosome-scale genome of P. emblica wild type 'Yingyu'. 'Yingyu' is an octopoid plant with a total of 104 chromosomes. In total, we assembled and clustered 480 Mb of the genome and constructed 26 pseudochromosomes (haplotypes) of P. emblica wild type 'Yingyu' that encompass 97.9% of the genome and demonstrate to have relatively high integrity. We annotated 31,111 genes found in the genome of P. emblica. We screened 5 different tissues for searching the tissue-specific expression candidate genes. Four unknown function candidate genes were expressed at high levels in the flowers while genes relating to the biosynthesis of gibberellins and cellulose were specifically expressed in the fruits. The ascorbate biosynthesis-related genes were screened on P. emblica 'Yingyu' genome. The high expression level of 2 GDP-mannose epimerases and one L-galactono-1,4- lactone dehydrogenases in the fruit may be related to the activity of absorbate biosynthesis in the fruit. The chromosome-level genomic data for P. emblica we report will be important for the development of molecular markers to facilitate the selection of superior cultivars for processing and pharmaceuticals.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607087","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

Comparative transcriptome and mutation analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene. 对肥胖2型糖尿病大鼠模型的胰岛进行转录组和突变比较分析，确定了脂钙蛋白2基因中一个频繁分布的无义突变。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-03-01 DOI: 10.1093/dnares/dsaf004

Norihide Yokoi, Naoki Adachi, Tomoki Hirokoji, Kenta Nakano, Minako Yoshihara, Saki Shigenaka, Ryuya Urakawa, Yukio Taniguchi, Yusaku Yoshida, Shigeo Yokose, Mikita Suyama, Tadashi Okamura

{"title":"Comparative transcriptome and mutation analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene.","authors":"Norihide Yokoi, Naoki Adachi, Tomoki Hirokoji, Kenta Nakano, Minako Yoshihara, Saki Shigenaka, Ryuya Urakawa, Yukio Taniguchi, Yusaku Yoshida, Shigeo Yokose, Mikita Suyama, Tadashi Okamura","doi":"10.1093/dnares/dsaf004","DOIUrl":"10.1093/dnares/dsaf004","url":null,"abstract":"Type 2 diabetes (T2D) is a multifactorial disease caused by insulin resistance and impaired insulin secretion from pancreatic β-cells, but the precise mechanisms remain to be elucidated. To identify primary genetic factors of T2D in a rat model, we performed comparative transcriptome and mutation analyses of the pancreatic islets between the obese Zucker fatty rat and the Zucker fatty rat-derived T2D model Zucker fatty diabetes mellitus (ZFDM) rat. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identified a nonsense mutation, c.409C > T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. We examined the relevance of the Lcn2 mutation with T2D in the ZFDM rat by using genome editing and genetic linkage analysis and confirmed that the Lcn2 mutation exhibits no significant association with the onset of T2D. Interestingly, we found that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate the pathophysiological roles of Lcn2 in a wide variety of phenotypes.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11976058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558525","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 temporary socially parasitic spiny ant Polyrhachis lamellidens and its host Camponotus japonicus. 临时群居寄生刺蚁polyrhachhis lamellidens及其寄主Camponotus japonicus的基因组组装。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-03-01 DOI: 10.1093/dnares/dsaf005

Hironori Iwai, Yu Kurihara, Nobuaki Kono, Masaru K Hojo, Katsushi Yamaguchi, Shuji Shigenobu, Mamiko Ozaki, Akiko Koto, Kazuharu Arakawa

{"title":"Genome assembly of the temporary socially parasitic spiny ant Polyrhachis lamellidens and its host Camponotus japonicus.","authors":"Hironori Iwai, Yu Kurihara, Nobuaki Kono, Masaru K Hojo, Katsushi Yamaguchi, Shuji Shigenobu, Mamiko Ozaki, Akiko Koto, Kazuharu Arakawa","doi":"10.1093/dnares/dsaf005","DOIUrl":"10.1093/dnares/dsaf005","url":null,"abstract":"Polyrhachis lamellidens is a temporary socially parasitic ant. The newly mated P. lamellidens queen takes over a colony of several Camponotus ant species and uses the labour of the host workers in the early stages of social parasitism. To facilitate genomic resources for these species, we assembled and annotated the chromosomal genome of P. lamellidens using the 10× Genomics linked-read and Hi-C sequencing, and the draft genome of its host, Camponotus japonicus, using long-read sequencing with the Revio system. The P. lamellidens chromosomal genome assembly is 214.1 Mb, 95.5% BUSCO completeness, and contains 13,703 protein-coding genes. The C. japonicus draft genome assembly is 314.2 Mb, 99.0% BUSCO completeness, and contains 11,207 protein-coding genes. Genome-wide phylogeny and synteny analysis confirmed the phylogenetic position of P. lamellidens and C. japonicus, and a high level of synteny with the genome of both ant species. In addition, P. lamellidens possesses nearly identical chemosensory proteins to its host, C. japonicus, and these genes tended to exhibit higher expression levels in the newly mated queen. The genome assemblies of P. lamellidens and its host C. japonicus provide a valuable resource for the molecular biological and bioinformatic basis for studying the strategy of social parasitism in ants.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558528","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