Complete Genome Sequencing of Halophilic Endophytic Aspergillus montevidensis, Strain ZYD4, Isolated from Alfalfa Stems Grown in Saline-Alkaline Soils

HomeMolecular Plant-Microbe Interactions®Vol. 35, No. 9Complete Genome Sequencing of Halophilic Endophytic Aspergillus montevidensis, Strain ZYD4, Isolated from Alfalfa Stems Grown in Saline-Alkaline Soils PreviousNext RESOURCE ANNOUNCEMENT OPENOpen Access licenseComplete Genome Sequencing of Halophilic Endophytic Aspergillus montevidensis, Strain ZYD4, Isolated from Alfalfa Stems Grown in Saline-Alkaline SoilsKaihui Liu, Xiaowei Ding, Guoliang Wang, and Wanting LiuKaihui Liu†Corresponding authors: K. Liu; E-mail Address: kaihhui168@sust.edu.cn, and X. Ding; E-mail Address: dxw518@sust.edu.cnSchool of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, ChinaSearch for more papers by this author, Xiaowei Ding†Corresponding authors: K. Liu; E-mail Address: kaihhui168@sust.edu.cn, and X. Ding; E-mail Address: dxw518@sust.edu.cnhttp://orcid.org/0000-0001-6060-2773School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, ChinaSearch for more papers by this author, Guoliang WangSchool of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, ChinaSearch for more papers by this author, and Wanting LiuSchool of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Kaihui Liu † Xiaowei Ding † Guoliang Wang Wanting Liu School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China Published Online:13 Jul 2022https://doi.org/10.1094/MPMI-12-21-0314-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementAspergillus is a complex group of ascomycetes comprising several hundred mold species, which are ubiquitously distributed in both natural and engineered ecosystems. This diverse group of filamentous fungi generally encompasses bioremediators, plant-growth-promoting fungi, biocontrol agents, and fungal endophytes. Many Aspergillus spp. have scientific and practical economic applications in food fermentation, environmental remediation, plant growth promotion, and biocontrol (Bano et al. 2018; Morales-Sánchez et al. 2021; Park et al. 2017; Salas-Marina et al. 2011). Among Aspergillus spp., the anamorph Aspergillus amstelodami (L. Mangin) was first catalogued in 1926 (Thom and Church 1926), and the teleomorph of this species was named A. montevidensis by Talice and Mackinnon in 1931. Previous studies showed that this microorganism can produce antibiotics and benzaldehyde derivatives with potent antimicrobial and antibiofilm properties (Darling et al. 1963; Fathallah et al. 2019). Our study found that A. montevidensis was capable of growing in hypersaline conditions supplemented with salt at 4.5 mol/liter (Ding et al. 2019). These findings suggest that A. montevidensis has potential applications in the fields of biological control and saline agriculture.Strain ZYD4 was isolated from alfalfa stems grown in saline and alkaline soils (Liu et al. 2017). The endophytic strain ZYD4 was cultivated using yeast extract-peptone-dextrose (Difco) and mycelia were collected for the genomic DNA extraction using the QIAamp DNA mini kit (Qiagen). The quality and concentration of the DNA samples were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific). Based on the morphological traits and phylogenetic analysis of the internal transcribed spacer, ZYD4 was identified as A. montevidensis (Fig. 1). For PacBio sequencing, a DNA library was constructed with an insert size of 20 kb using the SMRT Bell Template kit 1.0 (PacBio). For Illumina MiSeq sequencing, libraries were prepared with an insert size of 350 bp using an NEBNext Ultra DNA Library Prep Kit (NEB). The whole genome of strain ZYD4 was sequenced via the PacBio Sequel Systems and Illumina platform (Illumina, Inc.). The reads were trimmed and filtered using Trimmomatic v0.38 (Bolger et al. 2014) and de novo assembly was performed using the SPAdes genome assembler v3.12 (Bankevich et al. 2012). In total, 288,113 clean reads (average length: 11,548 bp) were obtained with an N50 read length of 13,464 bp, and the genome coverage was 125×. The final assembled genome contains 26,622,312 bases derived from nine contigs, with an N50 contig length of 3,879,884 and a G + C content of 49.1% (Table 1). The genome size is within the range of published Aspergillus genomes such as A. ruber, A. cristatus, A. chevalieri, and A. sydowii, which range from 26.2 to 35.4 Mb. The assembled genome contains 4,486 repeat sequences (0.81% of the genome) identified by Repeat Masker v4.0.5 and Tandem Repeats Finder v4.07b (Benson 1999; Saha et al. 2008). Protein-coding genes were predicted using the Augustus 2.7 program (Hoff and Stanke 2013). Genome-wide gene functional annotation was performed using the nonredundant protein database (NR), the Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam domains (Pfam), SwissProt, eukaryotic orthologous groups (KOG), and carbohydrate-active enzymes (CAZymes) databases, generating 6,061 predicted genes. We identified a total of 5,812 functional genes with NR annotation, 5,641 genes involved in different KEGG pathways, 4,142 genes with Pfam, 2,727 genes with SwissProt classification, and 1,903 genes with KOG items. In addition, 274 genes encoding CAZymes were assigned through the dbCAN2 web server (Zhang et al. 2018). We also predicted 189 transfer RNA genes, 43 ribosome RNA genes, and 19 other noncoding RNA genes. Genome analysis via the antiSMASH v5.1.2 revealed 21 putative gene clusters for secondary metabolite biosynthesis (Blin et al. 2019). Thirteen of these clusters encode nonribosomal peptide synthetases that catalyze the biosynthesis of various bioactive peptides. Four gene clusters encode type I polyketide synthases, which are responsible for the production of polyketides. The remaining clusters encode enzymes involved in the biosynthesis of terpene and siderophore.Fig. 1. Morphological and phylogenetic analysis of the strain ZYD4. A and B, Conidial head and cleistothecia of the fungus grown on potato dextrose agar media were stained with lactophenol cotton blue solution, visualized with a microscope (Olympus). C, Neighbor-joining phylogenetic tree of the fungus based on internal transcribed spacer sequences. Bootstrap values (expressed as percentages of 1,000 replications) are given at the nodes.Download as PowerPointTable 1. Summary statistics of the Aspergillus montevidensis strain ZYD4 genomeVariablesaStatisticsGenome sizes (bp)26,622,312Genome coverage125×Number of scaffolds9Maximum scaffold length (bp)6,508,595Average assembly length (bp)11,548N5013,464GC (%)49.1Number of predicted genes6,061Genes annotated by NR5,812Genes annotated by KEGG5,641Genes annotated by Pfam4,142Genes annotated by SwissProt2,727Genes annotated by KOG1,903Genes annotated by CAZyme274aDatabases: NR = nonredundant protein, KEGG = Kyoto Encyclopedia of Genes and Genomes, KOG = eukaryotic orthologous groups, and CAZyme = carbohydrate-active enzymes.Table 1. Summary statistics of the Aspergillus montevidensis strain ZYD4 genomeView as image HTML Data AvailabilityThe annotated whole-genome sequence of A. montevidensis, strain ZYD4, has been deposited at DNA Data Bank of Japan/European Nucleotide Archive/GenBank under the accession number JAJFZZ000000000. 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Nucleic Acids Res. 46:W95-W101. https://doi.org/10.1093/nar/gky418 Crossref, Medline, ISI, Google ScholarFunding: This study was supported by the National Natural Science Foundation of China (grant number 31970120). This work was partially funded by the Program of Agricultural Scientific and Technological Innovation of Shaanxi Province (2021NY-206) and by the program of Shaanxi University of Science and Technology (2018BJ-58 and 2019BJ-47).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. 9 September 2022ISSN:0894-0282e-ISSN:1943-7706 Download Metrics Article History Issue Date: 22 Sep 2022Published: 13 Jul 2022Accepted: 19 Apr 2022 Pages: 867-869 InformationCopyright © 2022 The Author(s).This is an open access article distributed under the CC BY-NC-ND 4.0 International license.Funding National Natural Science Foundation of ChinaGrant/Award Number: 31970120 Program of Agricultural Scientific and Technological Innovation of Shaanxi ProvinceGrant/Award Number: 2021NY-206 Shaanxi University of Science and TechnologyGrant/Award Number: 2018BJ-58Grant/Award Number: 2019BJ-47 KeywordsascomycetesAspergillusbiocontrolbioremediatorshypersalinesaline-alkaline soilThe author(s) declare no conflict of interest.PDF download