Computational protocol: De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment

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Protocol publication

[…] The transcriptome of M. indica cv. Shelly was sequenced according to Illumina Hiseq2000 and Trueseq protocols, at the Crown Institute for Genomics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine at the Weizmann Institute of Science, Rehovot, Israel. Eight libraries with total single-end RNA-seq reads 100 nucleotides in length were generated. The eight libraries contained the following sequences: 1) control RNA-seq of mango peel at time 0 h with 20,025,080 reads; 2) RNA-seq of mango peel treated by HWB at time 0 h with 20,202,891 reads; 3) control RNA-seq of mango peel at time 4 h with 21,622,332 reads; 4) RNA-seq of mango peel 4 h after HWB with 20,744,762 reads; 5) control RNA-seq of mango peel at 17 h with 20,916,444 reads; 6) RNA-seq of mango peel 17 h after HWB with 21,410,839 reads; 7) control RNA-seq of mango peel at 48 h with 20,687,358 reads; and 8) RNA-seq of mango peel 48 h after HWB with 21,230,696 reads. The transcriptome datasets are available in the NCBI Sequence Read Archive (SRA) under accession number SRX375390 and BioProject accession PRJNA227243. A new transcriptome was assembled from the 8.6-Gbp sequences by using Trinity software [], generating 57.544 contigs with N50 of 1,598 bp. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under accession no. GBCV00000000. The version described in the present paper is the first version, GBCV01000000.Tophat [], Bowtie2 [] and Cufflink packages [] were used to align the RNA-seq with the transcriptome and to calculate differentially expressed genes. The libraries were aligned with the mango transcriptome at alignment rates (mapped reads/total reads) of 90.84, 90.02, 89.48, 89.77, 90.70, 90.11, 90.25 and 90.35% for samples 1 to 8, respectively.The genes of M. indica cv. Shelly were annotated by using BLASTx [], after which their GO term [] was assigned by combining both BLASTx data and interproscan analysis [] by means of the BLAST2go software pipeline []. GO-enrichment analysis was performed by using Fisher’s exact test with multiple testing correction of FDR. Heat mapping and clustering of the genes were performed with the R software ggplots2 package []. […]

Pipeline specifications

Software tools Trinity, TopHat, Bowtie2, BLASTX, InterProScan, Blast2GO
Databases DDBJ TSA
Application RNA-seq analysis
Chemicals Chlorophyll