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

Abstract

Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The ‘Tunisia’ variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, 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 the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.

The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft‐ and hard‐seeded cultivars

“…We also identified many transcription factor families, such as MYB (16 genes), WRKY (five genes), AP2‐like (16 genes), MYC (two genes) and NAC (nine genes), that contained different proportions of SNPs and InDels (Figure b). Most of these transcription factors have been reported to play roles in regulating the seed hardness of pomegranates (Luo et al ., ; Xue et al ., ) and hawthorns (Dai et al ., ). In the comparison between ‘Tunisia’ and ‘Sanbai’, we detected a SNP (T‐C) at the 166‐bp position of the NAC ( PgL0137670 ) transcription factor coding sequence.…”

“…For example, gene expression analyses revealed that lignin and cellulose biosynthetic genes, including CCR, CAD, CelSy, SuSy, CCoA-OMT, MYB, WRKY and MYC, are differentially expressed between soft-and hard-seeded pomegranate varieties at different growth stages (e.g. fruit setting to ripening stages) (Xue et al, 2017;Zarei et al, 2016). Quantitative proteomics and microRNA sequencing results have suggested that genes altering the cell wall structure contribute to the differences in seed hardness between soft-and hard-seeded pomegranates (Luo et al, 2018;Niu et al, 2018).…”

Diversity of metabolite accumulation patterns in inner and outer seed coats of pomegranate: exploring their relationship with genetic mechanisms of seed coat development

“…The texture of the inner seed coat greatly affects acceptability to consumers. The preference of most consumers for soft-seeded pomegranates has accelerated the breeding of soft-seeded pomegranate cultivars and promoted mechanistic studies of the development of soft inner seed coats [2][3][4][5] . However, a complete overview of seed coat development in pomegranate has not yet been obtained.…”

Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness

“…In China, the best-known commercial soft-seeded pomegranate variety is Tunisia. This variety has been cultivated in China for more than 30 years 4 , resulting in cultivar depression. Thus, breeding new soft-seeded cultivars is imperative to meet market demands.…”