RNA-Seq-Based Transcriptome Profiling of Early Fruit Development in Chieh-qua and Analysis of Related Transcription Factors

Abstract

Abstract Background Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How.) early fruit development started post pollination. With the continuous expansion of the fruit, the soluble solid content of the fruit decreased. Although there was transcriptomics study on the early fruit development of cucumber, there was no report on the early fruit development of chieh-qua. In this study, fruit transcriptome of 0-, 3- and 7-days post pollination were compared. Results 104747 unigenes in the range of 201–14,209bp with a N50 length of 2119bp and 161282 transcripts were assembled from clean reads and comparing with 6 public databases for similarity searching. Principal component analysis separated the fruit ages into three groups. Compared with the 0 dpp (C), there were differences in the expression of 12982 and 6541 genes in the fruit tissue 3 dpp and 7dpp respectively. Compared with 3 dpp (B), there were 14314 differentially expressed genes in the fruit of 7dpp (A). According to the analysis of transcription factors, 213 nuigenes in MYB_superfamily was obtained. Among them 94 unigenes of MYB_superfamily differentially expressing in three stages. In the differential expression analysis of pairwise comparison, eight unigenes (Gene_id: TRINITY_DN32880_c1_g2, TRINITY_DN35142_c2_g2, TRINITY_DN32454_c11_g6, TRINITY_DN34105_c2_g7, TRINITY_DN32758_c3_g3, TRINITY_DN33604_c4_g10, TRINITY_DN34466_c3_g1, TRINITY_DN35924_c3_g2) are homologous to MYB59, MYB-GT3b, MYB18, MYB4, MYB108, MYB306, MYB340, MYB-bHLH13. And these unigenes are significant differences among the three groups of comparison. Further, MYB59 and MYB18 exhibited higher expression during the fruit pollinated for one week. While, MYB4, MYB-GT3b, MYB108 and MYB306 showed the highest expression levels in the fruits that have been pollinated for three days. Additionally, MYB340 and MYB-bHLH13 have showed higher expressions at the stage of unpollinated. Conclusion These results indicate that MYB59, MYB-GT3b, MYB18, MYB4, MYB108, MYB306, MYB340, MYB-bHLH13 could play crucial roles in chieh-qua fruit development, defence, and blossom. Overall, this study provides a basis for further investigations of the MYB_superfamily genes of early fruit expansion in chieh-qua.