Native Carica papaya: developing transcriptome resources to study water-deficit stress
Drought is the main single factor affecting crop production worldwide. Water-deficit stress causes severe impairment of cell homeostasis, resulting from osmotic and oxidative stress. However, plants have evolved complex mechanisms to deal with this stress. In the case of papaya (Carica papaya), commercial cultivars show susceptibility to drought stress. Given that Central America and the south of Mexico appear to be the center of origin of this species, the possibility exists that native populations collected in Yucatan may show better responses to drought than their commercial counterparts. In fact, our genotypes collected from undisturbed regions of Yucatan have proved to be physiologically more tolerant to water-deficit stress than those commercial cultivars commonly grown in Mexico. In order to obtain insights into the genetic mechanisms that C. papaya may use to deal with water-deficit stress; a transcriptome (RNA-Seq) approach was used with C. papaya leaves. Total RNA was obtained from two different genotypes, one that is susceptible to water deficit and another genotype that shows tolerance to water-deficit stress. Four cDNA libraries were constructed, from leaf tissue from plants from the two genotypes grown either under irrigation or under water deficit for 14 days. The quality of those libraries was confirmed by bioanalyzer (Agilent 2100). The cDNA libraries were then sequenced using MiSeq (Illumina platform). A total of 20,140,717 reads were obtained; these reads were pre-processed to remove adaptors and low-quality reads, and 11,804,864 clean sequences were assembled into 135,459 contigs. After removing isoforms and short contigs (<300 bp), a total of 29,070 sequences were identified as genes that represent the transcriptome of C. papaya. Sequence similarity searches against the Arabidopsis proteome revealed that 28,878 (99%) of 29,070 genes had significant matches (TAIR 10; bit-score ≥90), confirming the good quality of the transcriptome. Thus, these data provide a valuable source of information for improving our understanding of the molecular mechanisms by which C. papaya overcomes water-deficit stress.
Estrella-Maldonado, H., Ramírez Amaranta, G., Fuentes Ortíz, G., Góngora-Castillo, E., Peraza-Echeverría, S., Martínez, O. and Santamaría, J.M. (2019). Native Carica papaya: developing transcriptome resources to study water-deficit stress. Acta Hortic. 1250, 77-84
assembled, heatmap, leaf water potential, RNA-Seq