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Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps

The whole genome of Cordyceps pseudotenuipes 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 biosynthes...

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Autores principales: Lu, Yingling, Wang, Yi, Yuan, Xiaolong, Huang, Ou, Dong, Quanying, Li, Dandan, Ding, Shujin, Ma, Fuxian, Yu, Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505148/
https://www.ncbi.nlm.nih.gov/pubmed/36144248
http://dx.doi.org/10.3390/metabo12090844
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author Lu, Yingling
Wang, Yi
Yuan, Xiaolong
Huang, Ou
Dong, Quanying
Li, Dandan
Ding, Shujin
Ma, Fuxian
Yu, Hong
author_facet Lu, Yingling
Wang, Yi
Yuan, Xiaolong
Huang, Ou
Dong, Quanying
Li, Dandan
Ding, Shujin
Ma, Fuxian
Yu, Hong
author_sort Lu, Yingling
collection PubMed
description The whole genome of Cordyceps pseudotenuipes 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 Cordyceps. The genome-wide basic characteristics of C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris revealed unequal genome size, with C. cicadae as the largest (34.11 Mb), followed by C. militaris (32.27 Mb). However, the total gene lengths of C. pseudotenuipes and C. tenuipes were similar (30.1 Mb and 30.06 Mb). The GC contents of C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris genomes differed slightly (51.40% to 54.11%). AntiSMASH and local BLAST analysis showed that C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris 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, C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris had BGCs for the synthesis of dimethylcoprogen. C. pseudotenuipes, C. tenuipes, and C. cicadae had BGCs for the synthesis of leucinostatin A/B, neosartorin, dimethylcoprogen, wortmanamide A/B, and beauvericin. In addition, the SM BGCs unique to C. pseudotenuipes 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 Cordyceps and will facilitate the discovery of new biologically active SMs from the genus Cordyceps using heterologous expression and gene knockdown methods.
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spelling pubmed-95051482022-09-24 Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps Lu, Yingling Wang, Yi Yuan, Xiaolong Huang, Ou Dong, Quanying Li, Dandan Ding, Shujin Ma, Fuxian Yu, Hong Metabolites Article The whole genome of Cordyceps pseudotenuipes 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 Cordyceps. The genome-wide basic characteristics of C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris revealed unequal genome size, with C. cicadae as the largest (34.11 Mb), followed by C. militaris (32.27 Mb). However, the total gene lengths of C. pseudotenuipes and C. tenuipes were similar (30.1 Mb and 30.06 Mb). The GC contents of C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris genomes differed slightly (51.40% to 54.11%). AntiSMASH and local BLAST analysis showed that C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris 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, C. pseudotenuipes, C. tenuipes, C. cicadae, and C. militaris had BGCs for the synthesis of dimethylcoprogen. C. pseudotenuipes, C. tenuipes, and C. cicadae had BGCs for the synthesis of leucinostatin A/B, neosartorin, dimethylcoprogen, wortmanamide A/B, and beauvericin. In addition, the SM BGCs unique to C. pseudotenuipes 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 Cordyceps and will facilitate the discovery of new biologically active SMs from the genus Cordyceps using heterologous expression and gene knockdown methods. MDPI 2022-09-08 /pmc/articles/PMC9505148/ /pubmed/36144248 http://dx.doi.org/10.3390/metabo12090844 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lu, Yingling
Wang, Yi
Yuan, Xiaolong
Huang, Ou
Dong, Quanying
Li, Dandan
Ding, Shujin
Ma, Fuxian
Yu, Hong
Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title_full Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title_fullStr Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title_full_unstemmed Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title_short Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps
title_sort genomic comparative analysis of cordyceps pseudotenuipes with other species from cordyceps
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505148/
https://www.ncbi.nlm.nih.gov/pubmed/36144248
http://dx.doi.org/10.3390/metabo12090844
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