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. 2015 Feb 18:6:62.
doi: 10.3389/fpls.2015.00062. eCollection 2015.

Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening

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Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening

Mitzuko Dautt-Castro et al. Front Plant Sci. .

Abstract

Fruit ripening is a physiological and biochemical process genetically programmed to regulate fruit quality parameters like firmness, flavor, odor and color, as well as production of ethylene in climacteric fruit. In this study, a transcriptomic analysis of mango (Mangifera indica L.) mesocarp cv. "Kent" was done to identify key genes associated with fruit ripening. Using the Illumina sequencing platform, 67,682,269 clean reads were obtained and a transcriptome of 4.8 Gb. A total of 33,142 coding sequences were predicted and after functional annotation, 25,154 protein sequences were assigned with a product according to Swiss-Prot database and 32,560 according to non-redundant database. Differential expression analysis identified 2,306 genes with significant differences in expression between mature-green and ripe mango [1,178 up-regulated and 1,128 down-regulated (FDR ≤ 0.05)]. The expression of 10 genes evaluated by both qRT-PCR and RNA-seq data was highly correlated (R = 0.97), validating the differential expression data from RNA-seq alone. Gene Ontology enrichment analysis, showed significantly represented terms associated to fruit ripening like "cell wall," "carbohydrate catabolic process" and "starch and sucrose metabolic process" among others. Mango genes were assigned to 327 metabolic pathways according to Kyoto Encyclopedia of Genes and Genomes database, among them those involved in fruit ripening such as plant hormone signal transduction, starch and sucrose metabolism, galactose metabolism, terpenoid backbone, and carotenoid biosynthesis. This study provides a mango transcriptome that will be very helpful to identify genes for expression studies in early and late flowering mangos during fruit ripening.

Keywords: Mangifera indica L.; cell wall hydrolytic enzymes; ethylene; fruit quality; fruit ripening; mesocarp; transcriptome.

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Figures

FIGURE 1
FIGURE 1
Venn diagram of mango shared unigenes. Annotation was done according to the NCBI non-redundant (Nr), Swiss-Prot, COG, and KEGG databases and classified into Gene Ontology (GO). Overlapped unigenes are indicated in the intersections.
FIGURE 2
FIGURE 2
Top-hit species taxonomic distribution. Number of Unigenes matching the 30 top species using BLASTx in the NR database.
FIGURE 3
FIGURE 3
(A) Significantly enriched GO terms in the up-regulated transcripts ranked according to the p-value and number of genes. (B) Significantly enriched GO terms in the down-regulated transcripts ranked according to the p-value and number of genes.
FIGURE 4
FIGURE 4
(A) Expression ratio (Log2) obtained by qRT-PCR and RNA-seq of 10 selected genes associated to fruit ripening. ACO, 1-aminocyclopropane-1-carboxylate oxidase (comp59876); ETR1, ethylene receptor (comp46286); ERS1, ethylene receptor sensor (comp32379); EIN4, ethylene insensitive 4 (comp34039); PME, pectin methyl esterase (comp45079); PL, pectate lyase (comp63384); EXP, expansin (comp51667); AGAL, alpha-galactosidase (comp46653); LCBY, lycopene beta-cyclase (comp42574); and CHYB2, carotenoid beta-hydroxylase 2 (comp39312). GAPDH was used as a reference gene for normalization of qRT-PCR data. Bars represent the error standard (n = 3). (B) Correlation between the gene expression ratios obtained from RNA-seq data and qRT-PCR. The RNA-seq Log2 value of the expression ratio is shown in the y-axis and the qRT-PCR Log2 value of the expression ratio in the x-axis.

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