Plant Biology Europe is meeting for the EPSO/FESB 2016 Congress in Prague on June 26-30. At the event, Svetlana Shishkova, Universidad Nacional Autonóma de México, is presenting a poster on a study where CLC Genomics Workbench was used for data analysis.
Shishkova and her collaborators employed transcriptome and microtranscriptome analysis to explore the mechanisms of root apical meristem (RAM) maintenance and exhaustion in Cactaceae. They performed mRNA-seq and smallRNA-seq from primary root tips of a columnar cactus (Pachycereus pringlei) at distinct developmental stages and all processing of the reads was performed by CLC Genomics Workbench. You can find the full poster abstract below.
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Root transcriptome, microtranscriptome and gene regulatory networks involved in determinate root growth in desert Cactaceae
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 exhibits 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 desert environment. However, the 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 mRNA-seq and smallRNA-seq from primary root tips of a columnar cactus (Pachycereus pringlei) at distinct developmental stages. All processing of the reads was performed using CLC Genomics Workbench. Approximately 280 mln of paired 2×100 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 fully reconstructed. SmallRNA-seq reads were annotated and grouped using miRBase and the assembled transcriptome. The analysis of the virtual expression identified the transcripts and miRNAs differentially expressed in the developmental stages when the RAM still exists, and when it is exhausted. Gene regulatory networks (GRN) of P. pringlei root tip were built based on the Arabidopsis root tip GRN, and on the identification of putative cactus orthologues 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.