DNA Research最新文献_第3页

Diversity, evolution, and transcription of endogenous retroviruses in Chiroptera genomes. 内生逆转录病毒在翼翅目基因组中的多样性、进化和转录。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf021

Zhi-Jian Zhou, Yang Xiao, Jie Fang, Yong-Xiu Yao, Chen-Hui Yang, Laurent Dacheux, Dong-Sheng Luo, Ye Qiu, Xing-Yi Ge

{"title":"Diversity, evolution, and transcription of endogenous retroviruses in Chiroptera genomes.","authors":"Zhi-Jian Zhou, Yang Xiao, Jie Fang, Yong-Xiu Yao, Chen-Hui Yang, Laurent Dacheux, Dong-Sheng Luo, Ye Qiu, Xing-Yi Ge","doi":"10.1093/dnares/dsaf021","DOIUrl":"10.1093/dnares/dsaf021","url":null,"abstract":"Bats (Chiroptera) are a taxonomic group of immense biological and ecological importance. They are primary reservoirs and carriers of various zoonotic viruses. Endogenous retroviruses (ERVs) originate from ancient retroviruses invading the host, and ERV-derived sequences can function as regulatory elements which influence gene expression and contribute to both physiological and pathological processes. However, ERVs and ERV-like elements (ERVLEs) carried by bats have not been fully characterized. In this study, we systematically explored the ERVs in 61 bat species and identified 10,352 bat-ERVs and 5,884 bat-ERVLEs sequences, and these sequences covered 3 major virus genera and included 7 groups related to human ERVs in the subfamily Orthoretrovirinae. In particular, a relatively intact endogenous deltaretrovirus sequence was identified in Molossus molossus. Additionally, 358 bat-ERV and 33 bat-ERVLE were identified as recombinants. The integration time of bat-ERVs was estimated to be concentrated in the last 10 to 40 million years, indicating their role in shaping the bat genome during the long-term co-evolution of virus and host. Furthermore, carnivorous bats tended to have more relatively complete and younger ERVs compared to herbivorous bats. According to bat transcriptomes, we found that 1,385 bat-ERVs and 197 bat-ERVLEs had transcriptional potential in 20 different tissues of 25 bats, implying that bat-ERVs harboured actively expressed genes with potential functions. In summary, we comprehensively characterized bat-ERVs in terms of their evolution, types and potential functions, providing foundational data and a new perspective for further research on bat-ERVs.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977606","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 Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history. 对红杜鹃（Sauvagesia rhodoleuca）染色体尺度的基因组组装为其基因组进化和人口统计学历史提供了新的认识。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf022

Tian-Wen Xiao, Xin-Feng Wang, Zheng-Feng Wang, Hai-Fei Yan

{"title":"Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.","authors":"Tian-Wen Xiao, Xin-Feng Wang, Zheng-Feng Wang, Hai-Fei Yan","doi":"10.1093/dnares/dsaf022","DOIUrl":"10.1093/dnares/dsaf022","url":null,"abstract":"Sauvagesia rhodoleuca is an endangered species endemic to southern China. Due to human activities, only 6 fragmented populations remain in Guangdong and Guangxi. Despite considerable conservation efforts, its demographic history and evolution remain poorly understood, particularly from a genomic perspective. To address this, we assembled a chromosome-scale genome of S. rhodoleuca using Nanopore long-read sequencing, DNA short-read sequencing, RNA-seq, and Hi-C data. A total of 290.37 Mb of assembled sequences, accounting for 99.76% of the genome, were successfully anchored to 19 pseudo-chromosomes, achieving a BUSCO completeness of 98.40% and a long terminal repeat assembly index of 17.28. Genome annotation identified 26,758 protein-coding genes and 369 tRNA genes. Demographic analysis revealed a sharp decline in the effective population size of S. rhodoleuca beginning approximately 1 million years ago. Whole-genome duplication (WGD) analysis revealed that S. rhodoleuca experienced a whole-genome triplication (WGT) followed by a more recent WGD after diverging from the Rhizophoraceae. Genes retained from WGT and WGD events played key roles in the development and survival of S. rhodoleuca, as indicated by Gene Ontology analysis. The high-quality genome of S. rhodoleuca provides insights into its genomic characteristics and evolutionary history, offering a valuable resource for conservation and genetic management.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016517","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 survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference. 八种黄龙属植物的基因组调查和进化分析：SSR分析、线粒体特征和种群动态推断。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf020

Min Jiang, Qi Liu, Chao Jiang, Mingfei Zhan, Haibo Wen, Fengyue Shu, Lingli Xie, Tengteng Liu, Chenliang Ren, Wenqiao Tang, Kai Liu

{"title":"Genome survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference.","authors":"Min Jiang, Qi Liu, Chao Jiang, Mingfei Zhan, Haibo Wen, Fengyue Shu, Lingli Xie, Tengteng Liu, Chenliang Ren, Wenqiao Tang, Kai Liu","doi":"10.1093/dnares/dsaf020","DOIUrl":"10.1093/dnares/dsaf020","url":null,"abstract":"Freshwater bivalves are vital to aquatic ecosystems but face severe global threats. Understanding their genomic traits and evolution is crucial for effective conservation. This study conducted whole-genome sequencing on 8 Lamprotula species. These 8 species exhibited high genomic complexity, characterized by large genomes (1.89 to 2.65 Gb), high heterozygosity (>0.8), and high repeat content (>60%), estimated by k-mer analysis. Genome assemblies showed that L. caveata had the largest genome, while L. polysticta had the smallest. Furthermore, the assembled genome sizes of these 8 species exhibited an average increase of 22.58% compared to k-mer analysis estimates, largely due to their high heterozygosity. The mitochondrial genomes of these 8 species ranged in size from 15.69 kb to 17.13 kb, with GC contents varying from 36.36% to 40.77%. Phylogenetic analysis indicated early divergence of L. leai and L. caveata from the other 6 species. Pairwise Sequentially Markovian Coalescent analysis revealed population bottlenecks over the past million years, with L. rochechouarti showing more significant population size fluctuations during the Pleistocene Glacial Epoch. In summary, this study provides comprehensive genomic insights into 8 Lamprotula species, highlighting their high genomic complexity and evolutionary divergence, thereby establishing a crucial foundation for future conservation and genetic research efforts.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12454935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838502","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

Satellite DNAs rising from the transposon graveyards. 从转座子墓地升起的卫星dna。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-09-02 DOI: 10.1093/dnares/dsaf026

Eva Šatović-Vukšić, Patrik Majcen, Miroslav Plohl

{"title":"Satellite DNAs rising from the transposon graveyards.","authors":"Eva Šatović-Vukšić, Patrik Majcen, Miroslav Plohl","doi":"10.1093/dnares/dsaf026","DOIUrl":"10.1093/dnares/dsaf026","url":null,"abstract":"Repetitive DNA sequences, as transposable elements (TEs) and satellite DNA (satDNA) spread and diversify within host genomes, impacting genome biology in numerous ways. In the first part of this review, we emphasize the evolutionary importance of satDNAs and TEs, providing a short summary of their roles and the mechanisms by which they influence the structure and function of genomes. We also discuss the broad, complex, and extensive relationships between TEs and satDNAs. Following that, we bring together different mechanisms on the generation of satDNA from TE, as it has been demonstrated that almost any part of any type of TE can undergo tandemization and produce novel satDNAs. Importantly, we here present a hypothesis that would explain the existence of particular types of monomers, namely composite satDNA monomers which display multiple subsequent stretches of similarity to various TEs, for which the explanation was lacking so far. We propose that even highly shuffled and degraded TE remnants residing in heterochromatin 'TE graveyards' can give rise to new satDNA sequence monomers, transforming these genomic loci into DNA 'recycling yards'. Furthermore, we emphasize important evolutionary questions regarding the causes, mechanisms, and frequency of these occurrences.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12628747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193183","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

Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2. 基于参考的日本大麦（Hordeum vulgare ssp）染色体规模组装。Hayakiso的变种；

IF 3.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 10.1093/dnares/dsaf016

Tsuyoshi Tanaka, Yuhi Haraguchi, Takatomo Todoroki, Daisuke Saisho, Tomomi Abiko, Hiroomi Kai

{"title":"Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.","authors":"Tsuyoshi Tanaka, Yuhi Haraguchi, Takatomo Todoroki, Daisuke Saisho, Tomomi Abiko, Hiroomi Kai","doi":"10.1093/dnares/dsaf016","DOIUrl":"10.1093/dnares/dsaf016","url":null,"abstract":"Current advances in next-generation sequencing (NGS) technology and assembling programs permit construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex'. We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B, and D homoeologs, respectively), and rice. From the gene ontology analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as 'response to biotic and abiotic stress' and 'metabolic process'. Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512763","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

Manipulating alternative end-joining alters carbon-ion beam-induced genome mutation profiles in Arabidopsis thaliana. 操纵替代末端连接改变了碳离子束诱导的拟南芥基因组突变谱。

IF 3.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 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":"10.1093/dnares/dsaf014","url":null,"abstract":"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.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231562/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion. 近2个月来，珊瑚的分阶段基因组组装揭示了单倍型多样性和基因扩展的进化过程。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 10.1093/dnares/dsaf017

Takeshi Takeuchi, Yoshihiko Suzuki, Eiichi Shoguchi, Manabu Fujie, Mayumi Kawamitsu, Chuya Shinzato, Noriyuki Satoh, Eugene W Myers

{"title":"Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion.","authors":"Takeshi Takeuchi, Yoshihiko Suzuki, Eiichi Shoguchi, Manabu Fujie, Mayumi Kawamitsu, Chuya Shinzato, Noriyuki Satoh, Eugene W Myers","doi":"10.1093/dnares/dsaf017","DOIUrl":"10.1093/dnares/dsaf017","url":null,"abstract":"Gene family expansion illustrates a critical aspect of evolutionary adaptation. However, the mechanisms by which gene family expansions emerge and are maintained in the genome remain unclear. Here, we report de novo, nearly telomere-to-telomere (T2T), haplotype-phased genome assemblies of 2 coral species, Acropora tenuis and Acropora digitifera. By comparing haplotypes within a single individual and across species, we identified genomic regions spanning several megabases with highly disordered gene arrangements, termed non-syntenic regions (nSRs). In these nSRs, there are clusters of genes that emerged by lineage-specific gene family expansion. The gene repertoire within nSRs exhibits significant sequence diversity and distinct expression patterns, suggesting functional diversification. We propose that lineage-specific gene family expansion in nSRs occurs through recurrent tandem duplications mediated by non-allelic homologous recombination (NAHR) events, with nSRs serving as reservoirs for a diverse gene repertoire advantageous for survival. The nearly T2T-phased genomes provide new insights into the remarkable flexibility of genome organization and the evolution of gene family expansions.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12314368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545937","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

Dynamic integration and evolutionary trajectory of endogenous IHHNV elements in crustacean genomes. 内源IHHNV基因在甲壳类动物基因组中的动态整合与进化轨迹

IF 2.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 10.1093/dnares/dsaf018

Xiaoyun Zhong, Jianbo Yuan, Xiaojun Zhang, Shihao Li, Chengzhang Liu, Shuqing Si, Jie Hu, Anuphap Prachumwat, Kallaya Sritunyalucksana, Fuhua Li

{"title":"Dynamic integration and evolutionary trajectory of endogenous IHHNV elements in crustacean genomes.","authors":"Xiaoyun Zhong, Jianbo Yuan, Xiaojun Zhang, Shihao Li, Chengzhang Liu, Shuqing Si, Jie Hu, Anuphap Prachumwat, Kallaya Sritunyalucksana, Fuhua Li","doi":"10.1093/dnares/dsaf018","DOIUrl":"10.1093/dnares/dsaf018","url":null,"abstract":"Endogenous viral elements (EVEs) serve as molecular fossils that record the ancient co-evolutionary arms race between viruses and their hosts. In this study, by analyzing 105 host crustacean genomes, we identified 252 infectious hypodermal and haematopoietic necrosis virus-derived EVEs (IHHNV-EVEs), which include 183 ancient and 6 recently inserted EVEs. These IHHNV-EVEs are widely distributed among Decapoda, Thoracica, and Isopoda, with some of them exhibiting a syntenic distribution relative to neighboring host sequences, suggesting that the IHHNV or its ancestor are potential pathogens of these species with a long-time dynamic interaction during the evolutionary history. An expansion of IHHNV-EVEs was observed in decapoda genomes, reflecting a reinforced arm race between decapoda and IHHNV. Notably, we found that nearly all recent IHHNV-EVEs were laboratory contaminants, except for a single authentic integration in Penaeus monodon that persists intact across 16 samples from the 2 populations. These temporal dynamics-ancient genomic stabilization versus modern colonization activity-highlight that EVEs serve as dual archives: historical records of past conflicts and active participants in current evolutionary battles. Our findings redefine viral genomic colonization as a continuum, where ancient EVE fixation coexists with persistent integration processes, providing new insights into host-virus co-evolutionary trajectories.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12287923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692337","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

Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics. Thin-diaPASEF: diaPASEF用于在单次蛋白质组学中最大化蛋白质组覆盖。

IF 2.9 2区生物学

DNA Research Pub Date : 2025-07-04 DOI: 10.1093/dnares/dsaf019

Ryo Konno, Masaki Ishikawa, Daisuke Nakajima, Kaori Inukai, Osamu Ohara, Yusuke Kawashima

{"title":"Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics.","authors":"Ryo Konno, Masaki Ishikawa, Daisuke Nakajima, Kaori Inukai, Osamu Ohara, Yusuke Kawashima","doi":"10.1093/dnares/dsaf019","DOIUrl":"10.1093/dnares/dsaf019","url":null,"abstract":"Proteomics using mass spectrometry (MS) has significantly advanced, offering deep insights into complex proteomes. The timsTOF MS platform with its parallel accumulation-serial fragmentation (PASEF) technology has achieved high scan speeds and high-quality spectra. Bruker's timsTOF HT, which features TIMS-XR technology, offers an improved dynamic range and analysis depth, supporting high sample loadings. Moreover, various improvements to the data-independent acquisition method based on the PASEF technology (diaPASEF) have been reported. Despite these advancements, most high-level deep proteomic reports are based on the Orbitrap Astral and Orbitrap Exploris 480, and analytical systems using timsTOF MS still require improvement. Here, Bruker's timsTOF HT was used to validate and optimize key diaPASEF parameters, leading to the development of a Thin-diaPASEF method. This method provides a high quantitative accuracy and consistency. In our validation, 9,400 proteins were identified in a single shot from HEK cells (strictly controlled protein false discovery rate <1%), the highest number analysed by the timsTOF MS series using standard human cultured cells. Furthermore, by combining Thin-diaPASEF with an improved Lycopersicon esculentum lectin method, over 5,000 proteins were identified in a 24-sample/d analysis from the plasma, and we succeeded in constructing a system with high proteome coverage that can be used for biomarker discovery.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12314363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700299","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 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 : 2025-05-28 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":"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 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.","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/PMC12202052/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0