HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 6Genome Sequence Resource of Sarocladium terricola TR, an Endophytic Fungus as a Potential Biocontrol Agent Against Meloidogyne incognita Previous RESOURCE ANNOUNCEMENT OPENOpen Access licenseGenome Sequence Resource of Sarocladium terricola TR, an Endophytic Fungus as a Potential Biocontrol Agent Against Meloidogyne incognitaXueliang Tian, Tingting Sun, Runmao Lin, Rui Liu, Yuhong Yang, Bingyan Xie, and Zhenchuan MaoXueliang Tianhttps://orcid.org/0000-0001-5774-4631Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, P. R. ChinaSearch for more papers by this author, Tingting SunHenan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, P. R. ChinaInstitute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this author, Runmao LinInstitute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this author, Rui LiuInstitute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this author, Yuhong YangInstitute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this author, Bingyan Xie†Corresponding authors: Z. Mao; E-mail Address: [email protected], and B. Xie; E-mail Address: [email protected]Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this author, and Zhenchuan Mao†Corresponding authors: Z. Mao; E-mail Address: [email protected], and B. Xie; E-mail Address: [email protected]Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Xueliang Tian1 Tingting Sun1 2 Runmao Lin2 Rui Liu2 Yuhong Yang2 Bingyan Xie2 † Zhenchuan Mao2 † 1Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, P. R. China 2Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China Published Online:8 Apr 2022https://doi.org/10.1094/MPMI-11-21-0284-AAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleGenome AnnouncementSarocladium terricola TR, isolated from tomato root galls, possesses antagonistic activity against Meloidogyne incognita. The genome of S. terricola TR was sequenced to find the basis of this antagonistic activity.Many biocontrol agents have been isolated from Acremonium fungi to control animal and plant pathogens. Several secondary metabolites from Acremonium strains have been identified and found to exhibit useful biological activities. The Acremonium sp. strain bcc 31806 produces Acremoxanthones A and B, which are novel antibiotic polyketides against Gram-positive bacteria such as Staphylococcus aureus, Bacillus subtilis, and Enterococcus hirae (Isaka et al. 2009). The endophytic fungus Acremonium camptosporum W. Gams isolated from Bursera simaruba can synthesize six major heterodimeric polyketides that exhibit antioomycete and cytotoxic activities (Meléndez-González et al. 2015). The fungus A. implicatum can form endophytic associations with Brachiaria spp. and inhibit fungal pathogens such as Drechslera spp., which cause leaf spot disease (Kelemu and Takayama 1998; Kelemu et al. 2001). In addition, some Acremonium fungi have biocontrol ability against root-knot nematodes. A. striatum possesses both toxic and egg parasitic properties against M. incognita (Goswami and Singh 2004; Goswami et al. 2008). One A. implicatum strain with the strong chitinolytic and nematicidal activity showed great potential as a biocontrol agent against Meloidogyne incognita (Lin et al. 2013). The A. implicatum strain TR, an endophytic fungus from the root gall of tomato, possesses an antagonistic activity to M. incognita, which causes tomato root gall and reduces yield of tomato in greenhouses (Tian et al. 2014; Yao et al. 2015). Now, some species belonged to Acremonium spp. have been transferred to Sarocladium spp., and A. implicatum was renamed by Giraldo et al. (2015). The taxonomy of A. implicatum strain TR was also reevaluated by the whole genome phylogenetic analysis in this study and the current name should be Sarocladium terricola.Advances in genome sequencing, bioinformatics, and analytical chemistry have enabled the discovery of gene clusters related to metabolic products (Bills and Gloer 2016). To investigate the molecular basis and secondary metabolism of strain TR and gain insight into its antagonism against M. incognita, its whole genome was sequenced and analyzed.The fungus was cultured on potato dextrose agar (PDA) at 25°C for 7 days. One small plug of colonized media from PDA plates was put into flasks of potato dextrose broth and cultured at 25°C for 3 days on an orbital shaker set to 100 rpm. After 3 days, the mycelia were harvested by gravity filtration through KenAG Milk Filters and placed into one Lysing Matrix A tube (MP Biomedicals). For DNA isolation, the fungal tissue was disrupted using a FastPrep-24 tissue homogenizer; then, total DNA was extracted using a DNeasy Plant MiniKit (Qiagen) according to the manufacturer’s standard protocols. The DNA was used for library construction and for sequencing using Illumina HiSeq 2000 technology. The raw data with average insert sizes of 180 bp (coverage of approximately 100×), 800 bp (coverage of approximately 85×), and 5,000 bp (coverage of approximately 31×) was obtained and was assembled using Allpaths-LG revision 42305 (Gnerre et al. 2011) with default parameters. The total nuclear genome length of strain TR was approximately 30.18 Mb, with scaffold and contig N50 sizes of approximately 3.48 and 0.39 Mb, respectively (Table 1). The genome assembly consisted of 17 scaffolds and 127 contigs. Repeat Masker analysis detected a low percentage (1.05%) of repeat sequences in the nuclear genome. A phylogenetic tree was constructed using RAxML-NG v0.51b (Kozlov et al. 2019) with bootstrap value of 1,000 replicates and the TREE-PUZZLE v5.2 (Schmidt et al. 2002) with the Dayhoff model to identify the most closely related Sarocladium sp. (Supplementary Figure S1A). Based on the internal transcribed spacer sequences, the phylogenetic tree showed that the TR strain and three other S. terricola strains formed one clade (Supplementary Figure S1B). Hence, the strain TR was identified as S. terricola, which is in line with the results of Giraldo et al. (2015).Table 1. Genome summary statistics of Sarocladium terricola TRParametersaValueSize (bp)30,180,565GC content (%)54.0Number of scaffolds17Scaffold N50 (bp)3,477,858Number of contigs127Contig N50 (bp)389,533Number of protein-coding genes12,033Number of transfer RNAs89Repeat sequences (%)1.05Proteins with functional assignments68.4Complete BUSCOs (%)96.2aN50 = the sequence length of the shortest contig at 50% of the total genome length and BUSCO = benchmarking universal single-copy orthologs.Table 1. Genome summary statistics of Sarocladium terricola TRView as image HTML From the genome sequence, 12,033 protein-coding genes (Supplementary Table S1) were identified and functionally annotated using the methods from a previous study (Wang et al. 2016). The ab initio programs of Augustus and GeneMark-ES were used to predict genes with the parameter of “–species=Fusarium_graminearum” and the default parameters (Stanke et al. 2006; Ter-Hovhannisyan et al. 2008), respectively. To integrate the transcription start sites and homologous proteins from the Swiss-Prot database for gene prediction, the Eugene program was used to perform analysis (Schiex et al. 2001). Among these genes, 9,280 (77.12%) were identified by both Augustus v2.7 and GeneMark-ES v2.3f and the other 2,753 (22.88%) were identified by EuGene v4.1. Benchmarking universal single-copy orthologs (BUSCO v3) (Waterhouse et al. 2018) determined the gene set completeness of 96.2%. Functional annotation was successful for 8,227 (68.37%) genes, including 7,378, 7,644, and 3,927 genes annotated by Pfam domains (E-value cutoff of 1e−5), NCBI refseq fungi (E-value cutoff of 1e−50), and Swiss-Prot databases (E-value cutoff of 1e−50), respectively. Of these, 1,411 secreted proteins were identified, containing signal peptides supported by SignalP v4.0 (Petersen et al. 2011), TargetP v1.1 (Emanuelsson et al. 2000), Phobious v101 (Käll et al. 2004), and Predisi (Hiller et al. 2004). Among these secreted proteins, 117 were cysteine-rich proteins and 547 were small secreted proteins.The gene clusters of secondary metabolites were identified using antiSMASH (Blin et al. 2017). In total, 33 gene clusters were found, including 10 nonribosomal peptide synthetase (NRPS) clusters, 13 polyketide synthase (PKS) clusters, 1 PKS-NRPS hybrid cluster, and 4 terpene clusters (Supplementary Table S2). Among these clusters, two had homologous known gene clusters, including the PKS-NRPS hybrid cluster and one cluster containing two genes each of PKS and NRPS. Four genes in the PKS-NRPS hybrid cluster show similarity to genes in the Desmethylbassianin, Tenellin, and Fumosorinone biosynthetic gene clusters (Fig. 1A and B). Four and two genes in the cluster containing two genes of PKS and NRPS show similarity to the Acetylaranotin and Aspirochlorine biosynthetic gene clusters (Fig. 1A and B), respectively. The discovery of secondary metabolite clusters at the whole-genome level provided gene sources for future studies to explore the biological activities of the fungal natural products.Fig. 1. Gene cluster of secondary metabolites in Sarocladium terricola TR. A, Display of one polyketide synthase nonribosomal peptide synthetase (PKS-NRPS) hybrid cluster and its homologous known gene clusters. B, Domains of LIA77_09838 (the PKS-NRPS hybrid gene).Download as PowerPointIn summary, the genome of S. terricola TR, an endophytic fungus of tomato, contains multiple gene clusters of secondary metabolites predicted to suppress M. incognita. This genome provides insights into the molecular basis and secondary metabolism of S. terricola and supports further development of the fungus as a biocontrol agent against M. incognita. 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Lin are co-lead authors.Funding: This work was funded by the National Natural Science Foundation of China (31772214), Key Scientific Research Project of Higher Education of Henan Province (22A210012), China Agriculture Research System (CARS-25), Scientific and Technological Project of Xinxiang (GG2020007), and the Project of Plant Protection Key Discipline of Henan Province.The author(s) declare no conflict of interest. Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.DetailsFiguresLiterature CitedRelated Vol. 35, No. 6 June 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 20 May 2022Published: 8 Apr 2022Accepted: 9 Mar 2022 Pages: 505-508 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.FundingNational Natural Science Foundation of ChinaGrant/Award Number: 31772214Key Scientific Research Project of Higher Education of Henan ProvinceGrant/Award Number: 22A210012China Agriculture Research SystemGrant/Award Number: CARS-25Scientific and Technological Project of XinxiangGrant/Award Number: GG2020007Project of Plant Protection Key Discipline of Henan ProvinceKeywordsfungal endophytegenomegenomicsSarocladium terricolaThe author(s) declare no conflict of interest.PDF download