Changes in transcript abundance in the shoot apex highlight chloroplast development

In dicots, proplastids present in the central region of L2 layer of SAM that lack chlorophyll-binding proteins and thylakoid membranes, give rise to all green tissues of plants. These cells after a few cell divisions, reach to the periphery of the SAM, near the interface with the primordial leaves and acquire thylakoid membranes during this transition. We obtained [(i) proplastid containing, CZ, (ii) partially developed thylakoids containing, PZ and (iii) highly developed thylakoids containing, LP samples along this gradient with Laser microdissection, based on Chlorophyll fluorescence identification of cells. We performed RNA-seq with RNA obtained from these tissues, by using CEL sequencing (Cell Expression by Linear amplification and Sequencing) protocol. Similarly obtained RNA was also used for performing HT-qPCR on 190 genes from an initial list of 704 DEGs. Genes that passed the filters from the combined list were denoted as DEGs . CEL sequencing was performed on three different samples in triplicate with Illumina HiSeq 2500.