Genome sequence resources for three strains of the genus Clonostachys

Abstract

Objective

Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.

Data description

Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224 bp with a GC content of 48.58%, 58,114,960 bp with a GC content of 47.74% and 58,450,453 bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.

Objective

Most studies related to the genus Clonostachys have been focused on its powerful capacity as a biocontrol agent, especially of fungal pathogens. For example, Clonostachys rosea and C. chloroleuca are well-known destructive mycoparasites and can effectively control various plant diseases, caused by Fusarium species, Sclerotinia sclerotiorum and Botrytis cinerea [1,2,3]. Additionally, Clonostachys fungi are well known to produce a variety of secondary metabolites with various biological activities to show their pharmaceutical and agrochemical applications. Many of these compounds exhibit biological activities, such as cytotoxic, antimicrobial, antileishmanial, and antimalarial activities [4,5,6]. In the past decades, a zearalenone hydrolase encoded by C. rosea was discovered, and the zearalenone detoxification ability was proved to be important for the biocontrol of Fusarium graminearum [7,8,9,10].

It is remarkable as well that C. rosea is an important endophyte organism that, besides providing benefits to a wide range of host plants, can successfully mimic their chemical behavior [11, 12]. Some studies have shown the potential of C. rosea strains to promote the growth and health of diverse crops, such as tomato (Lycopersicon esculentum L.) [13], cucumber (Cucumis sativus L.) [14], wheat (Triticum durum Desf.) [15], pine (Pinus radiata D. Don) [16], and oil palm (Elaeis guineensis Jacq.) [17]. C. rosea was also classified as ‘plant-growth-promoting fungi’ (PGPF) [18]. Therefore, in-depth understanding of the molecular mechanisms underlying biocontrol of Clonostachys fungi will be conducive to developing sustainable strategies for management of fungal disease. In this regard, high-quality complete genome resources for Clonostachys fungi will be helpful.

Data description

In this study, we sequenced the genomes of three strains belonging to the genus Clonostachys, which were collected from the China General Microbiological Culture Collection Center (CGMCC). These strains were cultured on potato dextrose agar (PDA) for five days at 22 °C in the dark. Mycelia growing on the cellophane were harvested by scraping the plates with a flame-sterilized metal spatula, frozen in liquid nitrogen for 20 s, and stored at − 80 °C until use. The genomic DNA of strains was extracted using the cetyltrimethylammonium bromide (CTAB) method [19]. Quality control for genomic DNA (gDNA) was performed by measuring the absorbance at ratios 260/280 and 260/230 using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).

DNA samples were sent to Shanghai Biotechnology Corporation (Shanghai, China) for microbial whole genome sequencing. Three genome paired-end libraries were prepared for Illumina HiSeq 2500 System sequencing, yielding 27,300,124 short read pairs for strain CGMCC3.3655, 30,040,177 for strain CGMCC3.3657, and 33,506,775 for strain CGMCC3.4252 (Table 1 Data file 1–3). Fastp v0.20.0 was used to trim and filter the Illumina reads, then fastqc v0.11.9 and multiqc v1.8 were used to evaluate the reads’ quality [20,21,22]. After quality control, the short reads were used for de novo assembly by SPAdes v3.6.1 [23]. Potential mitochondrial genes and other possible contaminants from the genomes were filtered out using the Barrnap v0.9 [24]. The remaining contigs were filtered at 1,000 bp, and the quality of the assembly was visualized with QUAST v5.0.2 [25]. The resultant draft genomes were all > 58 MB in size. GC content was similar across all three genomes at 48%. However, the largest contig sizes varied with strain CGMCC3.3657 having the largest contig at 3,565,857 bp. Additionally, strain CGMCC3.3655 had the highest overall genome length at 58.5 Mb (Table 1 Data file 4–7). Transposable elements (TE) were identified by Tandem Repeat Finder (v4.04) [26] and The Extensive de novo TE Annotator (EDTA) [27]. The analysis revealed that 4.25% of the CGMCC3.3655 genome (LTR/Gypsy type: 1.5 Mb), 8.34% of the CGMCC3657 genome (LTR/Gypsy type: 1.9 Mb) and 3.99% of the CGMCC3.4252 (LTR/Gypsy type: 1.3 Mb) were composed of repetitive DNA (Table 1 Data file 7).

Table 1 Overview of all data files/data sets

Genome annotation was performed using the BRAKER v2.1.5 pipeline [28] based on GeneMark-ES version 4.68 [29] and Augustus v3.3.3 [30]. 17,770 protein-coding genes for strain CGMCC3.3655, 17,186 for strain CGMCC3.3657, and 17,779 for strain CGMCC3.4252 were predicted, respectively. To gain a functional gene annotation, we annotated whole-genome protein-encoding genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation of protein-coding genes was mainly performed by KAAS-KEGG Automatic Annotation Server (KEGG’s KAAS) (http://www.genome.jp/tools/kaas/) [31]. The Gene Ontology (GO) annotation of protein-coding genes was done using InterPro (v5.27) software [32]. The carbohydrate active enzymes (CAZymes) analysis was compared and annotated with the dbCAN database (https://bcb.unl.edu/dbCAN2/) by HMMER software (v3.3.2) [33]. The databases were pfam and Clusters Orthologous Groups (COG), which were compared using InterPro (version 5.27) [32] and diamond (v0.8.22) software [34], respectively. We identified a total of 11,835 proteins with Pfam domains, 3,950 genes with GO items, 5,051 genes involved in different KEGG pathways, 12,007 COG genes, and 237 CAZymes in the genome of strain CGMCC3.3655. There was also a total of 11,412 proteins with Pfam domains, 3,880 genes with GO items, 4,933 genes involved in different KEGG pathways, 11,600 COG genes, and 224 CAZymes in the genome of strain CGMCC3.3657. For strain CGMCC3.4252, we identified 11,851 proteins with Pfam domains, 3,960 genes with GO items, 5,057 genes involved in different KEGG pathways, 12,042 COG genes, and 236 CAZymes (Table 1 Data file 8–10). Their genome annotation completeness’s were estimated using benchmarking universal single-copy orthologs (BUSCO v4.1.4) with the fungi dataset [35], identifying 98.3 to 98.5% of the fungal orthologs (Table 1). With 1,000 bootstrap replicates, the phylogenetic tree was built in Molecular Evolutionary Genetics Analysis (MEGA) X software (v10.1.7) utilizing the neighbor-joining (NJ) method [36]. The phylogenetic analysis result based on the ATP citrate lyase (acl1) and the largest subunit of RNA polymerase II (rbp1) sequences showed that CGMCC3.3655, CGMCC3.4252 and other C. chloroleuca strains were grouped into one large branch with good support. But CGMCC3.3657 was clustered with members of C. rhizophaga (Table 1 Data file 7).

These genome sequences could contribute to the understanding of genetic and genomic diversities of Clonostachys fungi. It could also provide opportunities to analyze the molecular basis of their biocontrol activities.

Limitation

This data note was limited to the description of genomes of three Clonostachys strains. A larger collection is needed to help us better understand their genetic and biological characteristics.