Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites
As one of the commonly isolated endophytic fungi, <i>Alternaria</i> has been known for the production of numerous secondary metabolites (SMs). However, its detailed genomic features and SM biosynthetic potential have not been extensively studied thus far. The present work focuses on the...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-09-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/10/9/1789 |
| _version_ | 1827658578600656896 |
|---|---|
| author | Jianyun Tao Xuelian Bai Mingyuan Zeng Mengshi Li Zhe Hu Yunfen Hua Huawei Zhang |
| author_facet | Jianyun Tao Xuelian Bai Mingyuan Zeng Mengshi Li Zhe Hu Yunfen Hua Huawei Zhang |
| author_sort | Jianyun Tao |
| collection | DOAJ |
| description | As one of the commonly isolated endophytic fungi, <i>Alternaria</i> has been known for the production of numerous secondary metabolites (SMs). However, its detailed genomic features and SM biosynthetic potential have not been extensively studied thus far. The present work focuses on the whole-genome sequencing and assembly of an endophytic strain <i>Alternaria</i> sp. SPS-2 derived from <i>Echrysantha chrysantha</i> Lindl. and gene annotation using various bioinformatic tools. The results of this study suggested that the genome of strain SPS-2 was 33.4 Mb in size with a GC content of 51% and an N50 scaffold of 2.6 Mb, and 9789 protein-coding genes, including 644 CAZyme-encoding genes, were discovered in strain SPS-2 through KEGG enrichment analysis. The antiSMASH results indicated that strain SPS-2 harbored 22 SM biosynthetic gene clusters (BGCs), 14 of which are cryptic and unknown. LS–MS/MS and GNPS-based analyses suggested that this endophytic fungus is a potential producer of bioactive SMs and merits further exploration and development. |
| first_indexed | 2024-03-09T23:05:37Z |
| format | Article |
| id | doaj.art-29c6c7be62114a4eaa359e63c962e008 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T23:05:37Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-29c6c7be62114a4eaa359e63c962e0082023-11-23T17:53:16ZengMDPI AGMicroorganisms2076-26072022-09-01109178910.3390/microorganisms10091789Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary MetabolitesJianyun Tao0Xuelian Bai1Mingyuan Zeng2Mengshi Li3Zhe Hu4Yunfen Hua5Huawei Zhang6School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaCollege of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, ChinaSchool of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaSchool of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaSchool of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaSchool of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaSchool of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, ChinaAs one of the commonly isolated endophytic fungi, <i>Alternaria</i> has been known for the production of numerous secondary metabolites (SMs). However, its detailed genomic features and SM biosynthetic potential have not been extensively studied thus far. The present work focuses on the whole-genome sequencing and assembly of an endophytic strain <i>Alternaria</i> sp. SPS-2 derived from <i>Echrysantha chrysantha</i> Lindl. and gene annotation using various bioinformatic tools. The results of this study suggested that the genome of strain SPS-2 was 33.4 Mb in size with a GC content of 51% and an N50 scaffold of 2.6 Mb, and 9789 protein-coding genes, including 644 CAZyme-encoding genes, were discovered in strain SPS-2 through KEGG enrichment analysis. The antiSMASH results indicated that strain SPS-2 harbored 22 SM biosynthetic gene clusters (BGCs), 14 of which are cryptic and unknown. LS–MS/MS and GNPS-based analyses suggested that this endophytic fungus is a potential producer of bioactive SMs and merits further exploration and development.https://www.mdpi.com/2076-2607/10/9/1789endophytic fungus<i>Alternaria</i>genome sequencingantiSMASH analysisGNPSsecondary metabolite |
| spellingShingle | Jianyun Tao Xuelian Bai Mingyuan Zeng Mengshi Li Zhe Hu Yunfen Hua Huawei Zhang Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites Microorganisms endophytic fungus <i>Alternaria</i> genome sequencing antiSMASH analysis GNPS secondary metabolite |
| title | Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites |
| title_full | Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites |
| title_fullStr | Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites |
| title_full_unstemmed | Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites |
| title_short | Whole-Genome Sequence Analysis of an Endophytic Fungus <i>Alternaria</i> sp. SPS-2 and Its Biosynthetic Potential of Bioactive Secondary Metabolites |
| title_sort | whole genome sequence analysis of an endophytic fungus i alternaria i sp sps 2 and its biosynthetic potential of bioactive secondary metabolites |
| topic | endophytic fungus <i>Alternaria</i> genome sequencing antiSMASH analysis GNPS secondary metabolite |
| url | https://www.mdpi.com/2076-2607/10/9/1789 |
| work_keys_str_mv | AT jianyuntao wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT xuelianbai wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT mingyuanzeng wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT mengshili wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT zhehu wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT yunfenhua wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites AT huaweizhang wholegenomesequenceanalysisofanendophyticfungusialternariaispsps2anditsbiosyntheticpotentialofbioactivesecondarymetabolites |