Abstract
Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of Pterocarpus santalinus using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of P. santalinus for genome size, number of predicted genes, microsatellite repeat motifs, and nucleotide repeats. A near-complete chloroplast genome was assembled from the transcriptome reads. The proposed method requires less computational time and know-how, limited virtual memory, and is cost-effective when compared to whole-genome sequencing. Assembly of Cp genome from transcriptome data will enhance the resolution of phylogenetic studies through comparative plastome analysis, facilitate accurate species/genotype discrimination and accelerate the development of transplastomic plants with enhanced biotic and abiotic tolerance.
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The authors acknowledge the National Biodiversity Authority, Government of India for funding support.
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This study was funded by the National Biodiversity Authority, Government of India.
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SS conducted Cp genome assembly, annotation, analysis and drafted the manuscript; KU conceptualized the pipeline; MGD conceptualized the research, obtained funding, conducted transcriptome sequencing, prepared and finalized the manuscript. All authors have approved the manuscript.
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Senthilkumar, S., Ulaganathan, K. & Ghosh Dasgupta, M. Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. 3 Biotech 11, 393 (2021). https://doi.org/10.1007/s13205-021-02943-0
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DOI: https://doi.org/10.1007/s13205-021-02943-0