{"title":"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。","authors":"Shashi Kant, Sreyashi Das, Subhajeet Dutta, Kajal Mandal, Aditya Upadhyay, Aditya N Sarangi, Rajib Majumder, Sucheta Tripathy","doi":"10.1093/dnares/dsaf011","DOIUrl":null,"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 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.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"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\":null,\"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 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.</p>\",\"PeriodicalId\":51014,\"journal\":{\"name\":\"DNA Research\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-05-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"DNA Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/dnares/dsaf011\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"DNA Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/dnares/dsaf011","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Comparative genomics of Endophytic Fungi Apiospora malaysiana with related Ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.
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.
期刊介绍:
DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Comprehensive analysis of the functions of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes, gene families and genomes, 4) Computer algorithms and/or their applications relevant to structural and functional analysis of genes and genomes. The journal also welcomes novel findings in other scientific disciplines related to genomes.