Computational protocol: Microsatellites in the Genome of the Edible Mushroom, Volvariella volvacea

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Protocol publication

[…] The complete genome sequence of V. volvacea strain V23 was downloaded from the FTP site of GenBank. Information relating to the location of the gene models, introns, coding sequences (CDSs), 5′-untranslated-(5′-UTRs), 3′-untranslated-(3′-UTRs), and intergenic regions were obtained from the V. volvacea genome study group. 5′-UTRs are defined as the sequence located between a transcription start point and the beginning of the start codon of the transcript. 3′-UTRs are defined as the sequence between the stop codon and the last base of the transcript. Except introns, CDSs and UTRs, all the other regions in the genome are classified as intergenic regions. Coprinus cinereus, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus genome sequences used in this study (Table S1) (See Supplementary material available online at http://dx.doi.org/10.1155/2014/281912) were downloaded from the Joint Genome Institute (JGI) website.MISA software (http://pgrc.ipk-gatersleben.de/misa/) was used to locate and identify both perfect microsatellites and compound microsatellites interrupted by a certain number of bases. Mono- to hexanucleotide microsatellite motifs were identified using the following default parameters: mono- with at least 10 repeats; di- with at least six repeats; tri-, penta-, and hexa- with at least five repeats; the maximum number of bases between two microsatellites was 100 bp. [, ]. Unit patterns of repeats with circular permutations were considered as one type for statistical analysis. The same conditions were used to identify microsatellites in all the genome assemblies [, ]. To more accurately compare all the repeat types existing in different genomic regions, the relative abundance (mean of the number of microsatellites per Mb of the sequence analyzed) and the relative density (mean of the microsatellite length in bp per Mb of the sequence analyzed) were calculated separately []. Since longer microsatellites may display higher levels of polymorphism, primers for these loci were designed using the Primer3 software (http://frodo.wi.mit.edu/primer3/).Gene models having microsatellites in exons, introns, and UTRs were isolated and then scanned for InterPro domains and gene ontology (GO) annotation. The latter was used to assign each gene-encoded protein to one of the three defined categories (molecular function, biological process, or cellular component), and WEGO (Web Gene Ontology Annotation Plot) [] was used to plot the GO annotation data. […]

Pipeline specifications

Software tools MISA, Primer3, WEGO
Applications WGS analysis, qPCR
Organisms Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, Pleurotus ostreatus
Chemicals Nucleotides