Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i>
The whole genome of <i>Cordyceps pseudotenuipes</i> was sequenced, annotated, and compared with three related species to characterize the genome. The antibiotics and Secondary Metabolites Analysis Shell (antiSMASH) and local BLAST analysis were used to explore the secondary metabolites (...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/12/9/844 |
| _version_ | 1797484872950874112 |
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| author | Yingling Lu Yi Wang Xiaolong Yuan Ou Huang Quanying Dong Dandan Li Shujin Ding Fuxian Ma Hong Yu |
| author_facet | Yingling Lu Yi Wang Xiaolong Yuan Ou Huang Quanying Dong Dandan Li Shujin Ding Fuxian Ma Hong Yu |
| author_sort | Yingling Lu |
| collection | DOAJ |
| description | The whole genome of <i>Cordyceps pseudotenuipes</i> was sequenced, annotated, and compared with three related species to characterize the genome. The antibiotics and Secondary Metabolites Analysis Shell (antiSMASH) and local BLAST analysis were used to explore the secondary metabolites (SMs) and biosynthesis gene clusters (BGCs) of the genus <i>Cordyceps</i>. The genome-wide basic characteristics of <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> revealed unequal genome size, with <i>C. cicadae</i> as the largest (34.11 Mb), followed by <i>C. militaris</i> (32.27 Mb). However, the total gene lengths of <i>C. pseudotenuipes</i> and <i>C. tenuipes</i> were similar (30.1 Mb and 30.06 Mb). The GC contents of <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> genomes differed slightly (51.40% to 54.11%). AntiSMASH and local BLAST analysis showed that <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> had 31, 28, 31, and 29 putative SM BGCs, respectively. The SM BGCs contained different quantities of polyketide synthetase (PKS), nonribosomal peptide synthetase (NRPS), terpene, hybrid PKS + NRPS, and hybrid NRPS + Other. Moreover, <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> had BGCs for the synthesis of dimethylcoprogen. <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, and <i>C. cicadae</i> had BGCs for the synthesis of leucinostatin A/B, neosartorin, dimethylcoprogen, wortmanamide A/B, and beauvericin. In addition, the SM BGCs unique to <i>C. pseudotenuipes</i> were clavaric acid, communesin, and deoxynivalenol. Synteny analysis indicated that the scaffolds where the SM BGC was located were divided into more than 70 collinear blocks, and there might be rearrangements. Altogether, these findings improved our understanding of the molecular biology of the genus <i>Cordyceps</i> and will facilitate the discovery of new biologically active SMs from the genus <i>Cordyceps</i> using heterologous expression and gene knockdown methods. |
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| spelling | doaj.art-76cb6e41d52f4b169a9f1d67698b180f2023-11-23T17:44:39ZengMDPI AGMetabolites2218-19892022-09-0112984410.3390/metabo12090844Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i>Yingling Lu0Yi Wang1Xiaolong Yuan2Ou Huang3Quanying Dong4Dandan Li5Shujin Ding6Fuxian Ma7Hong Yu8Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, ChinaLaboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, ChinaLaboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, ChinaYunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, ChinaYunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, ChinaYunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, ChinaLaboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, ChinaLaboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, ChinaYunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, ChinaThe whole genome of <i>Cordyceps pseudotenuipes</i> was sequenced, annotated, and compared with three related species to characterize the genome. The antibiotics and Secondary Metabolites Analysis Shell (antiSMASH) and local BLAST analysis were used to explore the secondary metabolites (SMs) and biosynthesis gene clusters (BGCs) of the genus <i>Cordyceps</i>. The genome-wide basic characteristics of <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> revealed unequal genome size, with <i>C. cicadae</i> as the largest (34.11 Mb), followed by <i>C. militaris</i> (32.27 Mb). However, the total gene lengths of <i>C. pseudotenuipes</i> and <i>C. tenuipes</i> were similar (30.1 Mb and 30.06 Mb). The GC contents of <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> genomes differed slightly (51.40% to 54.11%). AntiSMASH and local BLAST analysis showed that <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> had 31, 28, 31, and 29 putative SM BGCs, respectively. The SM BGCs contained different quantities of polyketide synthetase (PKS), nonribosomal peptide synthetase (NRPS), terpene, hybrid PKS + NRPS, and hybrid NRPS + Other. Moreover, <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, <i>C. cicadae</i>, and <i>C. militaris</i> had BGCs for the synthesis of dimethylcoprogen. <i>C. pseudotenuipes</i>, <i>C. tenuipes</i>, and <i>C. cicadae</i> had BGCs for the synthesis of leucinostatin A/B, neosartorin, dimethylcoprogen, wortmanamide A/B, and beauvericin. In addition, the SM BGCs unique to <i>C. pseudotenuipes</i> were clavaric acid, communesin, and deoxynivalenol. Synteny analysis indicated that the scaffolds where the SM BGC was located were divided into more than 70 collinear blocks, and there might be rearrangements. Altogether, these findings improved our understanding of the molecular biology of the genus <i>Cordyceps</i> and will facilitate the discovery of new biologically active SMs from the genus <i>Cordyceps</i> using heterologous expression and gene knockdown methods.https://www.mdpi.com/2218-1989/12/9/844<i>Cordyceps</i>whole-genome sequencesecondary metabolitebiosynthesis gene cluster |
| spellingShingle | Yingling Lu Yi Wang Xiaolong Yuan Ou Huang Quanying Dong Dandan Li Shujin Ding Fuxian Ma Hong Yu Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> Metabolites <i>Cordyceps</i> whole-genome sequence secondary metabolite biosynthesis gene cluster |
| title | Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> |
| title_full | Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> |
| title_fullStr | Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> |
| title_full_unstemmed | Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> |
| title_short | Genomic Comparative Analysis of <i>Cordyceps pseudotenuipes</i> with Other Species from <i>Cordyceps</i> |
| title_sort | genomic comparative analysis of i cordyceps pseudotenuipes i with other species from i cordyceps i |
| topic | <i>Cordyceps</i> whole-genome sequence secondary metabolite biosynthesis gene cluster |
| url | https://www.mdpi.com/2218-1989/12/9/844 |
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