Transcriptome of Laser Micro Dissected Tissue from SAM of Tomato Reveals Genes Responsible for Chloroplast Biogenesis

Abstract

Chloroplast biogenesis was studied in the shoot Apical Meristem of tomato through employing mRNA sequencing of Laser micronized samples in different chloroplast developmental stages, by [1]. A stringent criterion was used for the determination of Differentially Expressed Genes. However this strategy masked most of the important genes that are involved in chloroplast biogenesis and thus undermined the importance of the study. Here, the same transcriptome data is being analyzed using a less stringent criteria of 1.5 fold expression between samples and minimum 2 mapping reads per gene to get 1266 DEGs. The DEGS were analyzed through their clustering, chloroplast localizations, functional domains, and their possible involvement in chloroplast development and by other various criteria to provide five sets of candidate genes that have a high probability to be involved in chloroplast biogenesis. Furthermore ~180 genes were cross checked for their expression through HT-qPCR on Fluidigm BIOMARK HD. Moreover the methodology is described in detail.