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.