| Phyllostachys edulis ‘Pachyloen’ is a new kind variety of Phyllostachys edulis with excellent characteristics,such as solid stem of the bottom,strong resistance,large biomass,stable genetic property.However,there is no systematic research on the genetic basis of thick wall bamboo germplasm traits up to now.Based on the Moso whole genome,the sixteen transcriptome of Phyllostachys edulis ‘Pachyloen’ and checked Phyllostachys edulis shoot samples at eight solar terms(in different developmental stages)were sequenced by using paired-end sequencing of Illumina HiSeqTM 2500.The samples were collected from September to April(next year).The eight transcriptome bioinformatics analysis results of Phyllostachys edulis ‘Pachyloen’ were obtained for the first time,and the main results are obtained as follows:1.The high quality data of satisfying bio-information analysis was obtained after the raw data being filtered and selected.The eight shoot buds of Phyllostachys edulis ‘Pachyloen’ generated data of 2.4-4.3 Gb.The eight shoot buds of checked Phyllostachys edulis generated data of 1.7-5.6 Gb.2.The rates of Phyllostachys edulis ‘Pachyloen’,checked Phyllostachys edulis mapping to the reference genome of Moso were 48.46-79.03%,66.02-80.97%,respectively.The gene numbers of mapping to the reference genes were both up to 27 000-28 000,which accounted for 88% of the total Moso genes.Gene expression profiles were analyzed by using software of Gene cluster.It was discovered that the two samples have the same development process.3.The whole expressed genes of the two samples were compared according to the change of solar terms.The numbers of special expressed genes of the two samples were 666-1 839 and 1 079-1 356,while the co-expressed gene number was 25 735-27 549.4.The differential expressed genes(DEGs)were regarded as the FDR≤0.001 and the absolute value of fold-change≥2 were filtered according to the value of RPKM(Reads Per Kb per Million reads).The DEGs of the co-expressed genes varied from 1 719 to 11 033.5.The selected genes were annotated using the GO(Gene Ontology)function database.The co-expressed DEGs were classified into 22 terms of biological process,16 terms of cell component,and 13 terms of molecular function.The special genes of Phyllostachys edulis ‘Pachyloen’ were classified into 20 terms of biological process,15 terms of cell component,and 12 terms of molecular function.The special genes of checked Phyllostachys edulis were classified into 19 terms of biological process,14 terms of cell component,and 10 terms of molecular function.6.The selected genes were analyzed according to the KEGG(Kyoto Encyclopedia of Genes and Genomes)Pathway database.The co-expressed DEGs were involved 158 pathways,69 of which were significant enrichment pathways.The special genes of Phyllostachys edulis ‘Pachyloen’ participated in 137 pathways,including 52 significant enrichment pathways.The special genes of checked Phyllostachys edulis involved 35 significant enrichment pathways of the 135 enrichment pathways.By analyzing these metabolic pathways using calculation of intersection union,27 pathways were screened.They might involve the pathways of related to the excellent germplasm traits of Phyllostachys edulis ‘Pachyloen’.And also,15 genes were selected which are involved in the formation of thick stem of Phyllostachys edulis ‘Pachyloen’.7.The new transcripts were predicted using software of Cufflinks.The spectrum of Phyllostachys edulis ‘Pachyloen’ and Phyllostachys edulis in each month was 11 494-17 639 and 6 449-17 835.The twelve kinds of AS(Alternative Splicing)events were predicted using ASprofile in each sample of each month.Among the all events of AS,the number of TSS and TTs was the most,accounting for 64.16-88.30% of the twelve AS events.Real time quantitative PCR(qPCR)have been carried out to verify the obtained trancriptome data,which accumulated molecular data for discovering the good germplasm traits of Phyllostachys edulis ‘Pachyloen’. |
PDF Full Text Request