Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum

Jun Qian, Haibin Xu, Jingyuan Song, Jiang Xu, Yingjie Zhu, Shilin Chen

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.

Original languageEnglish (US)
Pages (from-to)331-336
Number of pages6
JournalGene
Volume512
Issue number2
DOIs
StatePublished - Jan 10 2013
Externally publishedYes

Fingerprint

Reishi
Agaricales
Microsatellite Repeats
Genome
Nucleotides
Genes
Laccaria
Fungal Genome
Schizophyllum
Phanerochaete
Hydroxymethylglutaryl CoA Reductases
Genome Size
Gene Ontology
Intergenic DNA

Keywords

  • Agaricomycetes
  • Polyporales
  • Simple sequence repeats
  • SSRs

ASJC Scopus subject areas

  • Genetics

Cite this

Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum. / Qian, Jun; Xu, Haibin; Song, Jingyuan; Xu, Jiang; Zhu, Yingjie; Chen, Shilin.

In: Gene, Vol. 512, No. 2, 10.01.2013, p. 331-336.

Research output: Contribution to journalArticle

Qian, Jun ; Xu, Haibin ; Song, Jingyuan ; Xu, Jiang ; Zhu, Yingjie ; Chen, Shilin. / Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum. In: Gene. 2013 ; Vol. 512, No. 2. pp. 331-336.
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abstract = "Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04{\%} to 0.15{\%} of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4{\%} of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.",
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