Genome-Wide Analysis of WRKY and NAC Transcription Factors in Carica papaya L. and Their Possible Role in the Loss of Drought Tolerance by Recent Cultivars through the Domestication of Their Wild Ancestors.

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 Carica papaya 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 CpWRKYs genes and 25 of the 66 CpNACs 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 CpWRKY and CpNAC gene families. To corroborate this, we selected CpWRKY50 and CpNAC83.1 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) C. papaya genotypes to respond to drought (including the overexpression of the CpWRKY and CpNAC genes) was somehow reduced in the current commercial genotypes.

The interaction between exogenous IBA with sucrose, light and ventilation alters the expression of ARFs and Aux/IAA genes in Carica papaya plantlets.

KEY MESSAGE: The interaction between exogenous IBA with sucrose, light and ventilation, alters the expression of ARFs and Aux/IAA genes in in vitro grown Carica papaya plantlets. In vitro papaya plantlets normally show low rooting percentages during their ex vitro establishment that eventually leads to high mortality when transferred to field conditions. Indole-3-butyric acid (IBA) auxin is normally added to culture medium, to achieve adventitious root formation on in vitro papaya plantlets. However, the molecular mechanisms occurring when IBA is added to the medium under varying external conditions of sugar, light and ventilation have not been studied. Auxin response factors (ARF) are auxin-transcription activators, while auxin/indole-3-acetic acid (Aux/IAA) are auxin-transcription repressors, that modulate key components involved in auxin signaling in plants. In the present study, we identified 12 CpARF and 18 CpAux/IAA sequences in the papaya genome. The cis-acting regulatory elements associated to those CpARFs and CpAux/IAA gene families were associated with stress and hormone responses. Furthermore, a comprehensive characterization and expression profiling analysis was performed on 6 genes involved in rhizogenesis formation (CpARF5, 6, 7 and CpAux/IAA11, 13, 14) from in vitro papaya plantlets exposed to different rhizogenesis-inducing treatments. In general, intact in vitro plantlets were not able to produce adventitious roots, when IBA (2 mg L-1) was added to the culture medium; they became capable to produce roots and increased their ex-vitro survival. However, the best rooting and survival % were obtained when IBA was added in combination with adequate sucrose supply (20 g L-1), increased light intensity (750 µmol photon m-2 s-1) and ventilation systems within the culture vessel. Interestingly, it was precisely under those conditions that promoted high rooting and survival %, where the highest expression of CpARFs, but the lowest expression of CpAux/IAAs occurred. One interesting case occurred when in vitro plantlets were exposed to high levels of light in the absence of added IBA, as high rooting and survival occurred, even though no exogenous auxin was added. In fact, plantlets from this treatment showed the right expression profile between auxin activators/repressors genes, in both stem base and root tissues.

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber.

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.