De novo assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.)

Hui Xue, Shang-yin Cao, Haoxian Li, Jie Zhang, Juan Niu, Lina Chen, Fuhong Zhang, Diguang Zhao
Pomegranate (Punica granatum L.) belongs to Punicaceae. Pomegranate has been valued for its social, ecological, economic and aesthetic value and more lately for its health benefits. Especially, 'Tunisia' is widely popular, it has the qualities of soft-hardness seeds, big arils and can be easily swallowed. However, the molecular mechanisms of the hard and soft seed formation are not yet clear. We conducted a de novo assembly of the seed transcriptome of Punica granatum L., and revealed differential gene expression between the soft-seed and the hard-seed pomegranate cultivars. 35.1 Gb data was acquired in this study, including 280881106 raw reads. 132287 transcripts and 105743 representative unigenes were obtained by de novo assembly, approximately 13,805 unigenes (37.7%) of which are longer than 1,000 bp. According to unigenes of bioinformatics annotation, including the comparison of NR, Swiss-Prot, NT, KEGG, KOG, GO database, a total of 76806 unigenes were annotated. Among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of two pomegranate cultivars was related to lignin biosynthesis and metabolism, including some genes of laccase and peroxidase, WRKY, MYB, NAC and other transcription factors. In the hard-seed pomegranate, lignin related genes, cellulose synthesis related genes, and MYB transcription factor expression had high levels; flavonoids related genes and programmed cell death related gene expression in soft-seed pomegranate had slightly higher levels. Then some related genes were validated by qRT-PCR. This is the first transcriptome analysis of Punica granatum L. This transcription sequencing greatly enriched the pomegranate molecular database. The high quality SSRs generated in this study will aid the gene cloning of pomegranate in the future. It provides important insights into the molecular mechanisms underlying soft seed formation in pomegranate.
Xue, Hui, Cao, Shang-yin, Li, Haoxian, Zhang, Jie, Niu, Juan, Chen, Lina, Zhang, Fuhong and Zhao, Diguang (2018). De novo assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.). Acta Hortic. 1208, 131-146
DOI: 10.17660/ActaHortic.2018.1208.19
https://doi.org/10.17660/ActaHortic.2018.1208.19
pomegranate, seed hardness, lignin, transcription factor
English

Acta Horticulturae