3.4 Identification of isoforms and novel genes
The full-length and consensus sequences were identified and mapped onto the reference genome, resulting in over 96.37% mapping ratios (Supplementary Table 2). The mapped sequences were assembled using Stringtie, resulting in approximately 40,000 transcripts for each sample. The novel isoforms and novel genes were identified by comparing the assembled transcripts with the annotated transcripts of reference genome (Table 1). Similar numbers of isoforms of known genes were identified for the four samples. However, a larger number of novel isoforms of known genes were identified in GSB pathogen infected PI511890. More novel genes and their isoforms were observed in GSB pathogen infected PI511890 and Payzawat compared with their controls. These results indicated that GSB infection induces the transcription of more isoforms and novel genes, particularly in the resistant genotype.
Considering their potentially important roles in regulating the defense response of melon to GSB, the novel genes were further analyzed (Figure 3A). A total of 1,071 and 1,138 novel genes were specifically identified in Payzawat and PI511890 after infection, respectively. GO enrichment analysis showed that ATP hydrolysis activity was specifically enriched in infected Payzawat, while catalytic activity was specifically enriched in infected PI511890 (Supplementary Figure 3). Moreover, KEGG enrichment analysis showed that MAPK signaling pathway was specifically enriched for the novel genes in PI511890 but not for those in Payzawat (Figure 3B). These novel genes provide new insights into the defense response of melon to GSB.
Table 1.Numbers of isoforms and novel genes identified in the full-length transcriptome.