title: Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles.
abstract: Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of Ganoderma species. The current review carries out a detailed comparison of the nuclear genomes, mitochondrial genomes and transcriptomes from several Ganoderma species. Genes involved in biosynthetic pathways such as CYP450 genes and in cellular development such as matA and matB genes are characterized and compared in detail, as examples to demonstrate the usefulness of comparative genomic analyses for the identification of critical genes. Resources needed for future data integration and exploitation are also discussed.
authors: University of Göttingen, Büsgen-Institute, Department for Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, D-37077 Göttingen, Germany.
authors: Ursula
authors: U
authors: Kües
authors: Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave., Memphis, TN 38163, USA.
authors: David R
authors: DR
authors: Nelson
authors: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China. Electronic address: cliu6688@yahoo.com.
authors: Chang
authors: C
authors: Liu
authors: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China.
authors: Guo-Jun
authors: GJ
authors: Yu
authors: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
authors: Jianhui
authors: J
authors: Zhang
authors: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
authors: Jianqin
authors: J
authors: Li
authors: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
authors: Xin-Cun
authors: XC
authors: Wang
authors: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China.
authors: Hui
authors: H
authors: Sun
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D032902:Ganoderma / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D059467:Transcriptome / Q000235:genetics
chemical_list: D003577:Cytochrome P-450 Enzyme System
keywords: CYP450; Ganoderma; Mitochondrial genome; Transcriptome; Whole genome sequencing; matA; matB