| Summary: | A genome-wide analysis for two families of key transcription factors (TF; WRKY and NAC) involved in drought response revealed 46 WRKY and 66 NAC members of the <i>Carica papaya</i> genome. A phylogenetic analysis grouped the CpWRKY proteins into three groups (I, II a, b, c, d, e and III), while the CpNAC proteins were clustered into 15 groups. The conserved domains, chromosomal localization and promoter cis-acting elements were also analyzed. In addition, from a previous transcriptome study of two contrasting genotypes in response to 14 days of water deficit stress (WDS), we found that 29 of the 46 <i>CpWRKYs</i> genes and 25 of the 66 <i>CpNACs</i> genes were differentially expressed in response to the WDS. In the present paper, the native wild genotype (WG) (collected in its center of origin) consistently showed a higher expression (transcripts per million; TPM and fold change; FC) than the commercial genotype (CG) in almost all the members of the <i>CpWRKY</i> and <i>CpNAC</i> gene families. To corroborate this, we selected <i>CpWRKY50</i> and <i>CpNAC83.1</i> for further evaluation by RT-qPCR. Consistently, the WG showed higher relative expression levels (REL) after 14 days of WDS than the CG, in both the leaves and roots. The results suggest that the CpWRKY and CpNAC TF families are important for drought tolerance in this species. The results may also suggest that, during the domestication process, the ability of the native (wild) <i>C. papaya</i> genotypes to respond to drought (including the overexpression of the <i>CpWRKY</i> and <i>CpNAC</i> genes) was somehow reduced in the current commercial genotypes.
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