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. 2014 Sep 30;15(10):17667-85.
doi: 10.3390/ijms151017667.

De novo assembly and characterization of pericarp transcriptome and identification of candidate genes mediating fruit cracking in Litchi chinensis Sonn

Wei-Cai Li  1 , Jian-Yang Wu  2 , Hong-Na Zhang  3 , Sheng-You Shi  4 , Li-Qin Liu  5 , Bo Shu  6 , Qing-Zhi Liang  7 , Jiang-Hui Xie  8 , Yong-Zan Wei  9
Affiliations

De novo assembly and characterization of pericarp transcriptome and identification of candidate genes mediating fruit cracking in Litchi chinensis Sonn

Wei-Cai Li et al. Int J Mol Sci. .

Abstract

Fruit cracking has long been a topic of great concern for growers and researchers of litchi (Litchi chinensis Sonn.). To understand the molecular mechanisms underlying fruit cracking, high-throughput RNA sequencing (RNA-Seq) was first used for de novo assembly and characterization of the transcriptome of cracking pericarp of litchi. Comparative transcriptomic analyses were performed on non-cracking and cracking fruits. A total of approximately 26 million and 29 million high quality reads were obtained from the two groups of samples, and were assembled into 46,641 unigenes with an average length of 993 bp. These unigenes can be useful resources for future molecular studies of the pericarp in litchi. Furthermore, four genes (LcAQP, 1; LcPIP, 1; LcNIP, 1; LcSIP, 1) involved in water transport, five genes (LcKS, 2; LcGA2ox, 2; LcGID1, 1) involved in GA metabolism, 21 genes (LcCYP707A, 2; LcGT, 9; Lcβ-Glu, 6; LcPP2C, 2; LcABI1, 1; LcABI5, 1) involved in ABA metabolism, 13 genes (LcTPC, 1; Ca2+/H+ exchanger, 3; Ca2+-ATPase, 4; LcCDPK, 2; LcCBL, 3) involved in Ca transport and 24 genes (LcPG, 5; LcEG, 1; LcPE, 3; LcEXP, 5; Lcβ-Gal, 9; LcXET, 1) involved in cell wall metabolism were identified as genes that are differentially expressed in cracked fruits compared to non-cracked fruits. Our results open new doors to further understand the molecular mechanisms behind fruit cracking in litchi and other fruits, especially Sapindaceae plants.

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Figures

Figure 1
Figure 1
Characteristics of homology search of litchi pericarp unigenes against the NR database. (A) E-value distribution of the top BLAST hits for each unique sequence; (B) Similarity distribution of the top BLAST hits for each unique sequence; (C) Species distribution of the top BLAST hits for all homologous sequences.
Figure 2
Figure 2
Gene Ontology (GO) classification for all unigenes. All unigenes were aggregated into three main categories: biological process, cellular component and molecular function. Percentages are based on the proportion and number of genes in each set.
Figure 3
Figure 3
Clusters of Orthologous Groups (COG) function classification of all-unigene sequence. A total of 25,166 unigenes were classified into 25 COG categories.
Figure 4
Figure 4
Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG).
Figure 5
Figure 5
Comparison of transcript abundance levels between samples 1 and 2. Differentially expressed genes are shown in red and green; blue indicates genes that were not differentially expressed between the two samples.
Figure 6
Figure 6
Heat map diagram of candidate genes for fruit cracking in Litchi chinensis Sonn. The DEGs annotated in pathways related to water transport (A); gibberellin (GA) metabolism (B); abscissic acid (ABA) metabolism (C); Ca transport (D); cell wall metabolism (E) are shown.
Figure 7
Figure 7
Hypothesized mechanisms of fruit cracking in litchi.
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