利用比較基因體學與代謝體學研究臺灣新種蟲草的功能性基因及生物活性

Abstract

蟲草屬類群主要由昆蟲病原菌組成，其中多個物種在東亞被視為傳統藥材。近期研究中，Chuang 等人（2024）描述了來自臺灣的五個新種蟲草（Cordyceps hehuanensis、C. locastrae、C. malleiformis、C. pseudorosea 和 C. siangyangensis）。本研究初步探討了這五個新種與兩株 C. militaris 菌株的基因體多樣性，並進行全新的生物合成基因簇（BGCs）預測。本研究選取的蟲草屬物種以 Nanopore 長讀序列技術進行高品質基因體定序，並分析整個屬內的基因體特徵。從5098個直系同源基因 (single-copy orthologous) 獲得的基因體親緣演化樹所代表的演化關係，與從 ITS、nrLSU、tef1-α、rpb1和rpb2 片段獲得的多基因親緣演化樹具有相同的樹型結構。此外，average nucleotide identity (ANI)、average amino acid identity (AAI) 與percentage of conserved proteins (POCP) 的結果建議一致的蟲草屬物種界定。Biosynthetic gene cluster (BGC) 預測結果揭示了蟲草屬內代謝物的多樣性，其中如 beauvericin、beauverolide 和蟲草素等代謝物多樣性內演化存在一定的相關性。另外，Chuang（2020）對這七隻蟲草菌株的生物活性潛力進行了評估，特別探討了其蟲草素的生成能力。蟲草素為蟲草屬類群大量研究之生物活性物質，而該研究結果顯示僅有 C. militaris 和 C. hehuanensis 能夠生成蟲草素。然而近期研究指出，不產生蟲草素的蟲草屬物種同樣具有生物活性，這指出這些生物活性可能來源於其他代謝物。本研究假設臺灣新發現的蟲草屬物種中的生物活性可能來源於蟲草素以外的代謝物，並通過測定總酚含量、總黃酮含量、抗發炎活性和抗癌活性進行評估。在這些物種中，不產生蟲草素的 C. pseudorosea 顯示出與或超過產生蟲草素物種（C. militaris 和 C. hehuanensis）相當的抗癌潛力，而 C. locastrae、C. malleiformis 和 C. siangyangensis 則未顯示顯著的生物活性。 為了進一步了解這些物種間生物活性的差異，本研究使用 UHPLC-MS/MS 進行 untargeted 代謝體學分析，針對具細胞毒性和無細胞毒性物種（C. pseudorosea、C. locastrae 和 C. militaris）進行代謝物分析。主成分分析（PCA）和正交最小二偏差判別分析（OPLS-DA）揭示這三個物種間的明顯分群。在鑑定出的 208 種代謝物中，C. pseudorosea 顯著產生更多的 4-acetamidobutanoic acid、thalidomide、clozapine、biotin、salicylamide 和 (R)-(E)-sulforaphene，這些化合物可能作為潛在的生物標記物。值得注意的是，其中部分代謝物從未在真菌中報導過，故需要進一步分析或驗證以釐清預測結果。本研究鑑定了臺灣具生物活性的蟲草屬物種，並提供了其基因體和代謝體的全面見解。

The cordyceps-like species mainly consist of entomopathogenic fungi, with several species traditionally used in Eastern medicine. In a recent study, Chuang et al. (2024) described five new Cordyceps species (Cordyceps hehuanensis, C. locastrae, C. malleiformis, C. pseudorosea, and C. siangyangensis) from Taiwan. The present study initially explored the genomic diversity of these five new Cordyceps species together with two C. militaris strains and predicted their Biosynthetic gene clusters (BGCs) de novo. Selected Cordyceps species were sequenced using Nanopore long reads to provide high-quality genomes and analyze the general genomic features across the whole genus. The evolutionary relationship represented in the phylogenomic tree obtained from 5098 single-copy orthologous genes showed identical topology with the multi-locus phylogenetic tree obtained from ITS, nrLSU, tef1-α, rpb1, and rpb2 regions. Additionally, pairwise genome comparisons, including average nucleotide identity (ANI), average amino acid identity (AAI), and the percentage of conserved proteins (POCP), suggested a consistent pattern in their species delineation. Furthermore, BGCs were predicted to elucidate the metabolic diversity among Cordyceps species. The annotated BGCs, such as beauvericin, beauverolide, and cordycepin, exhibit a loss-based correlation with the evolutionary relationships within the genus. The bioactivity potential of these seven Cordyceps strains was assessed by Chuang (2020) by evaluating their cordycepin-production, a compound with significant medicinal potential. The results demonstrated that only C. militaris and C. hehuanensis were capable of producing cordycepin. However, recent findings suggested that non-cordycepin-producing Cordyceps species also exhibit bioactivities, indicating other metabolites may contribute to the observed bioactivities. The current study hypothesizes that metabolites other than cordycepin may contribute to the bioactivity observed in the Cordyceps species introduced in Taiwan. The bioactivities were evaluated by assessing total phenolic content, total flavonoid content, anti-inflammatory activity, and anti-cancer activity. Among these species, the non-cordycepin producing species, C. pseudorosea exhibited anti-cancer potential comparable to or exceeding that of cordycepin-producing species (C. militaris and C. hehuanensis), while other non-cordycepin species such as C. locastrae, C. malleiformis, and C. siangyangensis did not show significant bioactivities. To understand the bioactivity variation among these species, the present study, further conducted untargeted metabolomics using UHPLC-MS/MS to analyze the metabolomic profiles of cytotoxic and non-cytotoxic species, namely C. pseudorosea, C. locastrae, and C. militaris. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) revealed distinct groupings among the three species. Among the 208 identified metabolites, C. pseudorosea produced significantly more 4-acetamidobutanoic acid, thalidomide, clozapine, biotin, salicylamide, and (R)-(E)-sulforaphene compared to C. locastrae, suggesting these compounds as potential biomarkers. Notably, some of the identified metabolites have never been reported from fungal materials, and further analysis or validation is required to clarify the current prediction. Overall, this study identified bioactive Cordyceps species in Taiwan and provided comprehensive insights into their genomic and metabolomic profiles.