Abstract
The transcriptomes of five pear cultivars, ‘Hosui’ (P. pyrifolia), ‘Yali’ (P. bretschneideri), ‘Kuerlexiangli’ (P. sinkiangensis), ‘Nanguoli’ (P. ussuriensis), and ‘Starkrimson’ (P. communis) were sequenced at seven key fruit developmental stages, from fruit setting to maturation and fruit senescence after harvesting. In total, 33,136 genes that could be mapped by reads, were analyzed. Most gene expression cluster models showed a steadily decreasing trend. Gene expression patterns had obvious differences according to maturity type, that is, post-ripening cultivars were still vigorous at maturity, and showed a higher proportion of up-regulated genes; non post-ripening cultivars had a gradually decreasing tendency during fruit maturation. Meanwhile, differentially expressed genes related to fruit quality and development, such as stone cells, sugar, acid and hormones, were identified. Co-expression analysis revealed that several ethylene synthesis genes and polyphenoloxidase-related genes interacted with each other directly, and an indirect relationship was reflected between ethylene synthesis genes and ethylene response genes. In addition, the highly diverse SNPs represented the great differences between oriental and occidental pears. Understanding how RNA-seq based gene-expression patterns and differential gene expression contribute to fruit quality allows us to build models for gene-expression for fruit development of Pyrus species.
Highlights
The transcriptomes of five pear cultivars, ‘Hosui’ (P. pyrifolia), ‘Yali’ ( P. bretschneideri), ‘Kuerlexiangli’ (P. sinkiangensis), ‘Nanguoli’ (P. ussuriensis), and ‘Starkrimson’ (P. communis) were sequenced at seven key fruit developmental stages, from fruit setting to maturation and fruit senescence after harvesting
Even though up to 22 pear species have been identified[3], only five species are cultivated worldwide, four deriving from oriental countries, including P. pyrifolia, P. bretschneideri, P. sinkiangensis and P. ussuriensis, with only P. communis deriving from an occidental country
P. pyrifolia is cultivated in the south of China, P. bretschneideri in northern China, P. ussuriensis usually in the northeast region with extreme low temperatures, while P. sinkiangensis is only found in Xinjiang, and P. communis is cultivated in the north of China with cold climate, such as Beijing and Shandong province
Summary
RNA sequencing of different developmental stages of pear fruit in five cultivars. The transcriptomes of five representative cultivars: ‘Hosui’ (P. pyrifolia), ‘Yali’ (P. bretschneideri), ‘Kuerlexiangli’ (P. sinkiangensis), ‘Nanguoli’ (P. ussuriensis) and ‘Starkrimson’ (P. communis), which are the main cultivated species worldwide, were selected to reveal gene expression patterns and explore relationships between different fruit traits. Little difference was found in the percentage of aligned gene numbers accounting for clean reads during fruit developmental stages, it was relatively low for all cultivars at maturation or senescence (Table 1). One major reason might be that many genes have no expression or greatly decreased expression during fruit maturation Another natural reason could be low sequencing depth, and the limited sequencing data, 10 M reads with 49 bp length for each sample. Transcriptome sequencing revealed divergent gene expression patterns in pear fruit. No of clean reads 10,328,076 9,197,441 9,398,656 10,109,015 10,216,762 11,000,668 9,779,232 11,781,418 11,619,212 11,341,031 11,272,539 10,253,055 11,152,288 11,274,519 12,006,578 11,447,523 9,242,452 10,214,122 8,731,570 11,425,645 11,408,415 11,287,205 11,085,589 11,566,921 11,298,495 11,180,375 11,288,167 11,734,107 11,396,714 11,712,248 11,788,331 10,177,818 10,475,211 11,371,346 10,582,639
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