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.

叶绿体基因组测序是了解基因组进化和系统发育关系的重要工具。构建叶绿体基因组的可用方法包括叶绿体富集，然后是长重叠 PCR 或从全基因组数据集中提取和组装叶绿体特异性读数。在本研究中，我们提出了一种替代策略，即使用 bowtie2 aligner 程序从Pterocarpus santalinus的叶片转录组数据中提取和组装叶绿体特异性读数。将组装的基因组与已发表的P. santalinus叶绿体基因组进行比较基因组大小、预测基因的数量、微卫星重复基序和核苷酸重复。从转录组读数组装了一个近乎完整的叶绿体基因组。与全基因组测序相比，所提出的方法需要更少的计算时间和专有技术，有限的虚拟内存，并且具有成本效益。从转录组数据中组装 Cp 基因组将通过比较质体分析提高系统发育研究的分辨率，促进准确的物种/基因型区分，并加速具有增强的生物和非生物耐受性的转基因植物的发展。