Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales

Abstract

The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family.

Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordyceps nujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China

“…The sequencing library was built by the IlluminaTruseq DNA Sample Preparation Kit (BGI, Shenzhen, China), and the Illumina HiSeq 4000 Platform was applied to the PE2 × 150 bp sequencing. After data quality control, the unpaired, short, and low-quality reads were removed, and the clean reads were obtained ( Zhao et al 2021 ). Next, the reads of the mitogenome were collected from the clean data employing GetOrganelle v.1.6.2e, and the mitogenome was assembled using BLAST 2.2.30 and SPAdes.…”

“…For determining the phylogenetic location of the species, phylogenetic analyses were conducted with the combined sequence data of nrSSU, nrLSU, rpb1 , rpb2 , and tef-1 α ( Wang et al 2015 ; Wang et al 2020a ; Wang et al 2020b ), and ten protein-coding genes ( PCGs , atp6 , atp9 , cob , cox2 , nad1 , nad2 , nad3 , nad4 , nad4L , nad5 ) of mitogenomes, respectively ( Chen et al 2021 ; Zhao et al 2021 ). The Bayesian inference ( BI ) and the maximum likelihood ( ML ) methods were performed for the phylogenetic analyses by MrBayes v3.1.2 ( Ronquist and Huelsenbeck 2003 ) and RaxML 7.0.3 ( Stamatakis et al 2008 ).…”

“…The biogenetic analyses of the fungal mitochondrial genome could verify the genetically related species. NCBI has published the mitochondrial genomes of more than 680 fungi, including approximately 60 species of Hypocreales ( Chen et al 2021 ; Zhao et al 2021 ).…”

Phylogeny and systematics of the genus Clonostachys

“…Additional materials examined: China, Yunnan Province, Kunming City, Wild Duck Forest Park (25°13'N, 102°87′E, 2100 m above sea level), from soil on the forest floor, August 20, 2018, Yao Wang (living culture: YFCC 895); China, Yunnan Province, Kunming City, Songming County, Dashao Village (25°24'N, 102°55′E, 2697 m above sea level), from Ophiocordyceps highlandensis, August 25, 2018, De-Xiang Tang (living culture: YFCC 8591) (Zhao et al, 2021).…”

Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes

“…The advantages of mitochondria are that their evolution rate is faster than that of nuclear genes in most species. Each cell has multiple copies of the mitochondrial genome and higher A-T content [ 7 ]. Moreover, it also has the characteristics of conservation gene function [ 8 ].…”