Root transcriptome, microtranscriptome and gene regulatory networks involved in determinate root growth in desert Cactaceae.

MATVIENKO M.; BAUK K; RODRÍGUEZ-ALONSO G; LAS PEÑAS L; DUBROVSKY J.G; SHISHKOVA SVETLANA; LÓPEZ-VALLE M.L; NAPSUCIALY-MENDIVIL S

praga

Congreso; Plant BIology Europe; 2016

EPSO

Recent progress in New Generation Sequencing technology allows extending of the analysis of gene expression and regulatory networks for non-model species. Here we employed transcriptome and microtranscriptome analysis to explore the mechanisms of root apical meristem (RAM) maintenance and exhaustion in Cactaceae. In many species of desert Cactaceae from Cactiodeae subfamily the primary root exhibit determinate root growth, that is, the RAM exhaustion. Determinate growth of primary and lateral roots results in the formation of a compact root system that provides seedlings an advantage for survival in a desert environment. Yet, primary root growth of Opuntioideae subfamily members, that can inhabit either arid or mesic habitats, is more variable and could be determinate or indeterminate. We performed an mRNA-seq and sRNA-seq from primary root tips of a columnar cactus (Pachycereus pringlei) on distinct developmental stages. All processing of the reads was performed using CLC BIO Genomics Workbench. Appr. 280 mln of paired 2x100 nt mRNA-seq reads were de novo assembled into 49,045 contigs with 1,080 kb mean length, and 64% of the contigs were annotated with Blast2GO, InterPro Scan and KAAS tools. As an evidence of the assembly quality, the central metabolic pathways and CAM photosynthetic pathway were reconstructed. sRNA-seq reads were annotated and grouped using mirbase and the assembled transcriptome. Analysis of the virtual expression permitted to identify transcripts and miRNAs differentially expressed on the developmental stages when the RAM still exist and when it is exhausted. Gene regulatory networks (GRN) of P. pringlei root tip were built based on the Arabidopsis root tip GRN and identification of putative cactus orthologs of the Arabidopsis genes. Our results suggest that the GRN that operate in RAM of Angiosperms are mostly conserved. This work was partially supported by PAPIIT-UNAM (IN207115, IN205315) and CONACyT (CB240055, CB237430, FOINS219522) grants.