Genomic Comparative Analysis of Cordyceps pseudotenuipes with Other Species from Cordyceps

Abstract

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.

Genomic Comparison of Two Species of Samsoniella with Other Genera in the Family Cordycipitaceae

“…The results of the 14 genome-wide data analysis for 13 species of Cordycipitaceae indicated that C. cicadae region 87.1, region 56.2, region 27.1 and region 117.1 might exist to catalyze the synthesis of the BEA, dimethylcoprogen, wortmanamide A/B and viriditoxin, respectively, in agreement with our previous analysis of C. cicadae [28]. Among the 14 genomes, the potential gene clusters of acetylaranotin, bassianolide, dimethylcoprogen, epichloenin A, aspyridone A, curvupallide-B, fumosorinone, phomasetin, wortmanamide A/B, 4-epi-15-epi-brefeldin A, alternapyrone, asperfuranone, bikaverin, citrinin, fujikurin, solanapyrone D and viriditoxin were also excavated.…”

“…Previously, we conducted comparative genomic studies on the SM BGCs of Cordyceps and found that even related species of the same genus had different genome sizes, GC contents and assumed quantities of PKS, NRPS, hybrid PKS-NRPS, hybrid PKS-Other and terpene. Seven compounds, namely dimethylcoprogen, epichloenin A, wortmanamide A/B, phomasetin, fumosorinone, beauvericin, and viriditoxin, have been discovered as putative BGCs [28]. In this study, whole genomes of S. hepiali and S. yunnanensis YFCC 1527 were sequenced and annotated, and the basic characteristics and gene mining were compared with 14 genomes of 13 species belonging to 7 genera in the family of Cordycipitaceae (i.e., Akanthomyces, Cordyceps, Beauveria, Lecanicillium, Gamszarea, Samsoniella, and Simplicillium).…”

Genomic comparative analysis of Ophiocordyceps unilateralis sensu lato

“…Similar results were obtained that the sister species of Cordyceps, C. pseudotenuipes H. Yu, Q. Y. Dong, and Y. Wang and C. tenuipes (Peck) Kepler, B. Shrestha, and Spatafora, had the potential to synthesize dimethylcoprogen, epichloenin A, wortmanamide A/B, beauvericin, etc. (Lu et al, 2022). The number of NPRS-like, PR-PKS, Hybrid PKS-NRPS-Other and Hybrid By comparing the transcriptomes, Will et al (2020) pointed out that fusarin C might act as a virulence factor to alter ant behavior.…”