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

Authors: DAUTT-CASTRO, MITZUKO - Centro De Investigacion En Alimentaction Y Desarollo; OCHO-LEVVA, ADRIAN - Instituto Nacional De Medicina Genómica (INMEGEN), Secretaría De Salud, Distrito Federal, México C; CONTRERAS-VERGARA, CARMEN - Centro De Investigacion En Alimentaction Y Desarollo; PACHECO-SANCHEZ, MAGDA - Centro De Investigacion En Alimentaction Y Desarollo; CASAS-FLORES, SERGIO - Potosino Institute Of Scientific & Technological Researh; SANCHES FLORES, ALEJANDRO - Universidad Nacianal Autonoma De Mexico; Kuhn, David; ISLAS-OSUNA, MARIA - Centro De Investigacion En Alimentaction Y Desarollo

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2015
Publication Date: 2/18/2015
Citation: Dautt-Castro, M., Ocho-Levva, A., Contreras-Vergara, C.A., Pacheco-Sanchez, M.A., Casas-Flores, S., Sanches Flores, A., Kuhn, D.N., Islas-Osuna, M. 2015. Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. Frontiers in Plant Science. 6:62. doi:10.3389/flps.2015.0062.
DOI: https://doi.org/10.3389/flps.2015.0062

Interpretive Summary: The Subtropical Horticulture Research Station in Miami, Florida houses living collections of tropical and subtropical fruit trees, such as mango. These germplasm collections are resources for plant breeders, scientists studying fruit trees and nurseries hoping to expand their holdings to whom we distribute living plant material through our online request system (Germplasm Resource Information Network, http://www.ars-grin.gov/). It is important to understand the genetic diversity in our germplasm collection. By identifying important genes in the mango fruit ripening process, we can better understand the genetic diversity of our mango germplasm collection. In the context of plant breeding and germplasm collections, this understanding is very important for selection of parents in mango breeding programs. The information presented in the paper is valuable to GRIN users, breeders and stakeholders in regard to the correct germplasm material to request.

Technical 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.