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Integrated analysis of nutrient-associated transcriptome and metabolome of
developing chickpea seed
Arunima Sinha, Sushmita Biswas, Niranjan Chakraborty and Subhra Chakraborty*
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067,
India.
Storage organs in plants show remarkable diversity in reserve synthesis and accumulation
that affect growth, development, and productivity. They display diverse nutritional quality and
complex multistep development highly related to nutrient metabolism and transport as an
intense sink activity in plants. The synthesis and accumulation of each class of storage
component requires the coordination of many genes and proteins that encode the enzymes
of the respective pathways. Metabolic state and feedback regulation of low molecular weight
compounds influences the nutrient dynamics in developing seed. Chickpea, a legume,
known to have high nutrient composition and is an assimilator of various metabolites. RNAseq using Illumina Hi-seq 2000 paired-end sequencing technology was used to generate an
extensive map of nutrient-associated chickpea seed transcriptome. Further, metabolites
were extracted, derivatized, diluted and injected to GC-MS. The nutrient-responsive
transcriptome revealed a total of 192.3 million reads assembled into 191,487 total numbers
of contigs. Out of the total 60,584 transcripts, 6582 were found to be differentially expressed
at one or more developmental stages which were further categorized based on their putative
functions viz. metabolism, transcription, signaling, development and storage etc. Further,
Gene ontology (GO) analysis of differentially expressed transcripts was done using
Blast2GO. To complement the transcriptomic study, metabolome study revealed
identification of diverse compound ranging from non polar to polar metabolites including
sugars, sugar phosphates, organic acids, amino acids. The parallel analysis between the
quantification of metabolites and determination of transcripts aid in constructing a metabolic
atlas summarizing the dynamics of nutrient synthesis, accumulation and utilization on central
metabolic pathways in developing chickpea seeds.