title: De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification.
abstract: Auricularia polytricha (Mont.) Sacc., a type of edible black-brown mushroom with a gelatinous and modality-specific fruiting body, is in high demand in Asia due to its nutritional and medicinal properties. Illumina Solexa sequenceing technology was used to generate very large transcript sequences from the mycelium and the mature fruiting body of A. polytricha for gene discovery and molecular marker development. De novo assembly generated 36,483 ESTs with an N50 length of 636 bp. A total of 28,108 ESTs demonstrated significant hits with known proteins in the nr database, and 94.03% of the annotated ESTs showed the greatest similarity to A. delicata, a related species of A. polytricha. Functional categorization of the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed the conservation of genes involved in various biological processes in A. polytricha. Gene expression profile analysis indicated that a total of 2,057 ESTs were differentially expressed, including 1,020 ESTs that were up-regulated in the mycelium and 1,037 up-regulated in the fruiting body. Functional enrichment showed that the ESTs associated with biosynthesis, metabolism and assembly of proteins were more active in fruiting body development. The expression patterns of homologous transcription factors indicated that the molecular mechanisms of fruiting body formation and development were not exactly the same as for other agarics. Interestingly, an EST encoding tyrosinase was significantly up-regulated in the fruiting body, indicating that melanins accumulated during the processes of the formation of the black-brown color of the fruiting body in A. polytricha development. In addition, a total of 1,715 potential SSRs were detected in this transcriptome. The transcriptome analysis of A. polytricha provides valuable sequence resources and numerous molecular markers to facilitate further functional genomics studies and genetic researches on this fungus.
authors.affiliation: Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Lianfu
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Xiuzhi
authors.initials: X
authors.lastname: Fan
authors.affiliation: Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China; Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Yinbing
authors.initials: Y
authors.lastname: Bian
mesh_terms: D001487:Basidiomycota / Q000235:genetics*; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000096:biosynthesis* / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D056726:Genetic Association Studies; D053858:Metabolic Networks and Pathways / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005656:Fungal Proteins