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Characterization of Pythium transcriptome and gene expression analysis for different fermentation stage

ABSTRACT: We performed transcriptome assembly and gene expression analysis using short-read sequencing technology combined with a tag-based digital gene expression (DGE) system. The results generated a total number of 13,288,892 reads (accumulated length of 1,196,000,280 nt), 169,579 contings and 23,796 unigenes. Based on similarity search with known proteins, a total of 9,398 unigenes were identified with a cut-off E-value of 10-5. Assembled sequences were annotated with gene descriptions, such as gene ontology (GO) and clusters of orthologous group terms (COG). In addition, we obtained approximately 6 million raw tags and a larger number of genes at different fermentation stages (48 h, 100 h and 144 h). The related genes of growth characteristic and lipid biosynthesis were analyzed in detail. Some genes associated with the lipid biosynthesis were selected randomly to confirm digital gene expression (DGE) results by quantitative real-time PCR (qRT-PCR). The transcriptome improves our genetic understanding of Pythium splendens RBB-5 greatly and makes a large number of available gene sequences for further study. Notably, the transcriptome and DGE profiling data of Pythium splendens RBB-5 provide the comprehensive insight into gene expression profiles at different fermentation stages and lay a foundation for further study of optimizing lipid content and growth speed at the molecular level.

ORGANISM(S): Globisporangium splendens

PROVIDER: GSE43320 | GEO | 2014/12/30

SECONDARY ACCESSION(S): PRJNA185420

REPOSITORIES: GEO

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Project description:Although pear is an important edible fruit species, the current available genomic information is limited. Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of pear, especially fruit development and maturation.Using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system, de novo transcriptome assembly and gene expression analysis of P. bretschneideri were performed at an unprecedented depth (5.47 gigabase pairs). Approximately 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes. The unigenes comprised 17,619 contig clusters and 72,608 singletons and were an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.6% of the unigenes (31,215) were annotated against KEGG into 121 known metabolic or signaling pathways. DGE libraries of five different developmental fruit stages were constructed and analyzed, and the gene expression variations between two consecutive stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Extensive transcriptome and DGE profiling data have been obtained from the deep sequencing of the Chinese white pear, which can serve as an important public information platform for gene expression, genomic, and functional genomic studies in P. bretschneideri and which provides comprehensive gene expression information at the transcriptional level that could facilitate understanding of the molecular mechanisms in fruit development and maturation.

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Characterization of Pythium transcriptome and gene expression analysis for different fermentation stage

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