DNA ResearchPub Date : 2025-05-31DOI: 10.1093/dnares/dsaf014
Jing Long, Jian Zhao, Jingmin Chen, Jianing Ding, Xiao Liu, Zhe Li, Po Bian, Ting Wang, Wenjie Jin, Xihong Lu, Yifan Zhang, Libin Zhou, Yan Du
{"title":"Manipulating alternative end-joining alters carbon-ion beam-induced genome mutation profiles in Arabidopsis thaliana.","authors":"Jing Long, Jian Zhao, Jingmin Chen, Jianing Ding, Xiao Liu, Zhe Li, Po Bian, Ting Wang, Wenjie Jin, Xihong Lu, Yifan Zhang, Libin Zhou, Yan Du","doi":"10.1093/dnares/dsaf014","DOIUrl":"https://doi.org/10.1093/dnares/dsaf014","url":null,"abstract":"<p><p>DNA double-strand breaks (DSBs) repair via POLQ-mediated alternative end-joining (Alt-EJ) is error-prone and mutagenic. However, Alt-EJ is often inhibited by classical nonhomologous end-joining (C-NHEJ) or homologous recombination, the precise impact of Alt-EJ on plant genome instability remains unclear. Here, we employed carbon-ion beam (CIB) which induce complex DSBs to bias cellular repair strategies toward Alt-EJ; additionally, a specific genetic background of C-NHEJ deficiency (lig4-4) Arabidopsis thaliana line and the POLQ-deficient (teb-3 and teb-8) were combined to further amplify the mutagenic effects of CIB mediated by Alt-EJ. The lig4-4 exhibited higher sensitivity to CIB than POLQ-deficient lines. teb-8 exhibited constitutive DNA damage response (DDR), whereas DDR in lig4-4 was strictly induced by CIB. At genome scale, lig4-4 showed substantial changes in the insertion and deletion (InDels) mutation profile, with a higher proportion and larger size of InDels as well as greater microhomology dependence than wild-type. In contrast, teb-8 showed moderate changes, including increased single-base InDels and complex mutations, but lacking >30 bp InDels. Loss-of-function in LIG4 and POLQ resulted in a higher proportion of high-impact genome mutations than wild-type even at lower doses. These findings offered essential insights for the development of a novel repair pathway-driven heavy ion beam mutagenesis system.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192480","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}
{"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":"10.1093/dnares/dsaf011","url":null,"abstract":"<p><p>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 that pathogenic fungi, especially N. oryzae, show a reduced number of secondary metabolites biosynthesis and catabolic genes, 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 the 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 cellulolytic enzyme production. These findings position endophytes as valuable resources for cellulolytic enzyme research and broader bio-industrial applications.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","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}
DNA ResearchPub Date : 2025-05-28DOI: 10.1093/dnares/dsaf013
{"title":"Correction to: Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.","authors":"","doi":"10.1093/dnares/dsaf013","DOIUrl":"10.1093/dnares/dsaf013","url":null,"abstract":"","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"32 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217469","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 : 2025-05-28DOI: 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":"10.1093/dnares/dsaf009","url":null,"abstract":"<p><p>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% to 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% to 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 thiamin biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while most Pseudomonas and Xanthomonas plasmids are 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.</p>","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/PMC12142739/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"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":"10.1093/dnares/dsaf008","url":null,"abstract":"<p><p>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 3 pig breeds across altitudes: the Diannan small-ear pig (DSE ~500 m), the Baoshan pig (BS ~1500 m), and the Changdu Tibetan Pig (CT ~3500 m). 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.</p>","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/PMC12137898/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA ResearchPub Date : 2025-05-28DOI: 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":"10.1093/dnares/dsaf010","url":null,"abstract":"<p><p>The New World Ampullariids, encompassing the ecologically important genera Pomacea and Marisa, are gastropods 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.</p>","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/PMC12131234/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
DNA ResearchPub Date : 2025-05-28DOI: 10.1093/dnares/dsaf015
Kritika M Garg, Dolyce H W Low, Geraldine Lee, Benjamin P Y-H Lee, Ian H Mendenhall, Frank E Rheindt, Gavin J D Smith, Balaji Chattopadhyay
{"title":"Hybrid genome assembly of the widespread bat Rhinolophus lepidus provides insights into susceptibility to SARS-CoV-2 infection and climate change threat.","authors":"Kritika M Garg, Dolyce H W Low, Geraldine Lee, Benjamin P Y-H Lee, Ian H Mendenhall, Frank E Rheindt, Gavin J D Smith, Balaji Chattopadhyay","doi":"10.1093/dnares/dsaf015","DOIUrl":"10.1093/dnares/dsaf015","url":null,"abstract":"<p><p>Bats are known reservoirs for many viruses of zoonotic potential and can tolerate or clear infections efficiently. They are important hosts for multiple coronaviruses and harbour ancestral lineages of coronaviruses known to cause diseases in both humans and animals. In this study, we describe a high-quality hybrid genome assembly of the Blyth's horseshoe bat Rhinolophus lepidus. It is a widespread species and an important cell-line model system for studying virus entry and replication. We used a combination of short Illumina reads and long reads from Oxford Nanopore to assemble the genome, with N50 of 5.3 Mb and Benchmarking Universial Single-Copy Orthologs (BUSCO) score of ~94%. The Angiotensin-converting enzyme 2 receptor responsible for the entry of severe acute respiratory syndrome coronaviruses (SARS and SARS-CoV-2) was highly conserved within bats, especially the region responsible for virus entry into the cell. In total, 50% of the amino acids necessary for virus entry were conserved between humans and R. lepidus. We observed an effect of past climatic conditions on the effective population size with drastic population size reduction in the past 50,000 years. This study adds to the growing list of bat genomes which are important resources to understand the co-evolution of bats and viruses and the mechanism by which bats can tolerate and clear infections effectively.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210177","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}
DNA ResearchPub Date : 2025-05-28DOI: 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":"<p><p>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.</p>","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}
{"title":"Whole-genome sequencing of the ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae).","authors":"Ayako Gotoh, Atsushi Toyoda, Takahiro Yamabe, Takehiko Itoh","doi":"10.1093/dnares/dsaf012","DOIUrl":"10.1093/dnares/dsaf012","url":null,"abstract":"<p><p>The ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae) serves as a valuable model organism for investigating queen-specific traits, such as reproductive capacity and longevity, at the cellular and molecular levels. To support future research on queen traits using molecular techniques, including genome editing and multi-omics data analyses, we performed whole-genome sequencing of this species. The genome size of C. osakensis was estimated to be 284 Mb, with a heterozygosity of 0.26%. Annotation revealed the presence of 16,053 protein-coding genes. Furthermore, using the coding sequences annotated in this study, we reanalyzed previously obtained transcriptome data to identify highly expressed genes in the reproductive organs of queens and males. This data will contribute to a deeper understanding of the genetic mechanisms underlying reproductive strategies in ants.</p>","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/PMC12167229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112699","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":"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":"<p><p>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.</p>","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}