De novo Assembly and Functional Annotation of the Loquat Fruit Transcriptome during Veraison

Abstract: Loquat (Eriobotrya japonica Lindl.) belongs to Eriobotrya in Rosaceae. Loquat fruits are usually yellow or white flesh. Carotenoids are the main pigments accumulated in mature loquat fruit. In this work, the flesh at different fruit developmental stages of three loquat cultivars with distinct color flesh (Huangjinkuai, HJK, salmon flesh; Jiefangzhong, JFZ, yellow flesh and Baiyu, BY, white flesh) were sampled, differentially expressed genes were analyzed using transcriptome sequencing technology. The transcriptomes of loquat fruits generated 11.92 Gb Clean Data. Among De novo assembly of 51,934 Unigenes, 26,447 Unigenes were successfully annotated by blast searches against various databases including NR, Swiss-Prot, KEGG, COG, KOG, GO and Pfam database. Based on Unigene database, gene structure was analyzed, 4,438 SSR markers were obtained by the analysis of SSR. Moreover we found 11,096 unigenes sequences containing SNP sites by the analysis of SNP, among them, many SNP sites on 13 unigenes of carotenoid biosynthetic pathways were identified. In BY-HJK, BY-JFZ and JFZ-HJK pairwise comparison there are 507, 457 and 613 SNP sites respective on these carotenoid biosynthetic pathways unigenes. 3,438 differentially expressed genes were identified by pairwise comparison of three flesh-color type loquat varieties HJK, JFZ and BY. Functional annotation and enrichment analysis of all differentially expressed genes showed that 12 genes may be related to the accumulation of carotenoid, among which 9 genes were related to carotenoid metabolism and 3 PAP genes were associated with plastid lipid protein.

Key Words: Loquat; carotenoid; plastid; transcriptome