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Fig. 1 | BMC Plant Biology

Fig. 1

From: RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

Fig. 1

Flowchart of de novo assembly and analysis of Arundo donax leaf transcriptome. After the fully expanded leaf sampling, total RNA extraction and cDNA library preparation was carried out. The RNA integrity and quality analysis were performed (blue) before the Illumina sequencing. The sequencing output data were subjected to quality control of both reads and bases and data filtering (orange) in order to remove containing adapter reads or reads of low quality. Clean data were used for the de novo assembly of transcripts choosing the single k-mer approach (k = 25) (green), and the pre-assembled transcriptome obtained was further processed with Corset for hierarchical clustering by removing transcripts redundancy and by selecting the longest transcripts as unigenes (yellow). The quality of the assembly was assessed by mapping back the reads onto the filtered transcriptome (grey). Finally, gene functional annotation, CDS/EST prediction, differential expression analysis, phylogenetic analysis and GO and KEGG enrichment were carried out

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