mRNA-Seq Assisted Discovery of Genetic Programs Involved in Root Meristem Activity and Exhaustion in a Sonoran Desert Cactaceae

Determinate growth of the primary root implies early root apical meristem (RAM) exhaustion and cell differentiation at the root tip. It is characteristic for the majority of species from Cactoideae subfamily of Cactaceae and considered to be an adaptation to arid habitats.

To characterize genes involved in root meristem maintenance and determinate root growth in cardón Pachycereus pringlei, we employed mRNA-seq using Illumina GAII, de novoassembly of contigs using CLC Genomic Workbench, and annotation by protein similarity. We estimated differential gene expression in primary root tips between the initial growth phase (when RAM is present), and the terminal growth phase (when RAM is exhausted).

The 85 nt reads were assembled into about 26,000 contigs with an average length of 1035 nt. Three different expression scenarios for selected transcription factors were observed: (a) similar to Arabidopsis, (b) differential expression of the putative homeologs and (c) opposite to Arabidopsis. Some homologs of PIN auxin efflux carriers were induced in the primary root tip during either initial or terminal growth phases, while most genes involved in cytokinin synthesis and metabolism were induced during the terminal phase.

Significant conservation was revealed for the amino acid sequence and RNA expression patterns of various proteins. Moreover, subfunctionalization is suggested for putative homeologs of SHR and SCR. The data also suggest that the P. pringlei primary root tip with exhausted meristem performs functions similar to those of the differentiation zone of Arabidopsis root. Supported by PAPIIT-UNAM (IN204912).