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RNA-seq Based Gene Repertoire Survey And Symbiosis-related Gene Analysis Of The Arbuscular Mycorrhizal Fungus Gigaspora Rosea

Posted on:2017-01-10Degree:DoctorType:Dissertation
Country:ChinaCandidate:N W TangFull Text:PDF
GTID:1220330485478180Subject:Microbiology
Abstract/Summary:PDF Full Text Request
Arbuscular mycorrhizal fungi(AMF), belonging to the monophylum Glomeromycota, form an unique mutually beneficial symbiosis, called arbuscular mycorrhiza(AM), with most land plants. These fungi confer their host plants with better nutrition and resistence to biotic or abiotic stresses, thus have many implications in ecology and agriculture. Despite the great importance, the mechanisms underlying the development and functioning of AM are largely unknown, mainly due to the complexity in the biology and genetics of AMF. The recent release of R. irregularis genome and transcriptome provided the first glance at its genetic make-up and gene expression dynamics across different developmental stages. However, considering the large phylogenetic diversity observed in the Glomeromycota, whether the features identified in R. irregularis(Glomerales), are well conserved in all AMF is still unknown. To make this clear and broaden our knowledge on AMF, the species Gigaspora rosea, belonging to the order of Diversisporales, was chosen to be investigated here since its different phylogenetic status and physiological traits compared with those of R. irregularis. By using RNA sequencing(Illumina) and related bioinformatic tools, the transcriptome of G. rosea was assembled and analyzed, obtaining the following results:1. According to the physiological traits of G. rosea, we developed suitable protocols for the preparation of biological samples representative of different developmental stages. Using these protocols, the fungal RNA quantity and quality were significantly enriched, especially in the symbiotic materials.2. Using CLC genomics workbench, original RNA sequencing reads were firstly sorted based on their origins and then the fungal reads were de novo assembled into 86332 nonredundant virtual transcripts(NRVTs) with an average length of 643 bp. only 15346 transcripts could be annotated by blastx against the Refseq protein database, suggesting the existence of many lineage-specific orphan genes in this fungus. GO and KOG functional annotation showed that the signaling involved genes were significantly enriched in G. rosea. Although metabolism pathway analysis(KEGG) indicates that most primary metabolism pathways are active in G. rosea, few genes are still missing. The loss of these genes could have caused the obligatory biotrophy of AMF. The deep annotation of gene categories that could be related to its specific physiological traits reveals several features that are well conserved in the whole AMF group. These features could be linked to the specific biology and evolutionary strategy of AMF. In addition, phylogenomics of basal fungi clearly showed the close relationship between Glomeromycota and Mucoromycotina fungi.3. Gene expression profiling revealed hundreds of transcripts were differentially expressed during the intraradical symbiotic stage of G. rosea, compared with the extraradical stage. These upregulated transcripts are mainly involved in oxidationreduction process, proteolysis and transmembrane transport. By comparing the G. rosea transcriptomes in two divergent host plants(medicago and brachypodium), we found a high proportion of transcripts displayed similar expression profile in both hosts. Considering the phylogenetic distance between these two hosts, this similarity suggests AMF might have adopted a very conserved gene expression regulation strategy to handle the AM symbiosis in all hosts. Through comparison with the R. irregularis transcriptomics, a small set of genes remnant of the ancient fungal gene ―toolkit‖ for the AM symbiosis was identified. The annotation of this small set of genes suggests the signalling mediated by secreted proteins, the nutrients exchange played by transporters and the fatty acid elongation and modification processes might have played important roles in all AM symbiosis.Considering the scarcity of genomic data in Glomeromycota, this study undoubtedly lays the first foundation for G. rosea gene functional characterization in the future, but also enables the comparison of transcriptomes or genomes within Glomeromycota and among other related fungi possible.
Keywords/Search Tags:Arbuscular mycorrhizal fungi(AMF), Arbuscular mycorrhiza(AM), transcriptomics, gene expression profiling
PDF Full Text Request
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