Senthilkumar Shanmugavel, Ulaganathan Kandasamy, Ghosh Dasgupta Modhumita
Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India.
Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007 Andhra Pradesh India.
3 Biotech. 2021 Aug;11(8):393. doi: 10.1007/s13205-021-02943-0. Epub 2021 Aug 2.
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 using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of 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.
The online version contains supplementary material available at 10.1007/s13205-021-02943-0.
叶绿体基因组测序是理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现有方法包括叶绿体富集，随后进行长重叠PCR，或从全基因组数据集中提取和组装叶绿体特异性读段。在本研究中，我们提出了一种从[具体植物名称]的叶片转录组数据中提取和组装叶绿体特异性读段的替代策略，使用bowtie2比对程序。将组装的基因组与已发表的[具体植物名称]叶绿体基因组在基因组大小、预测基因数量、微卫星重复基序和核苷酸重复方面进行比较。从转录组读段中组装出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业知识，虚拟内存有限，且具有成本效益。从转录组数据中组装叶绿体基因组将通过比较质体基因组分析提高系统发育研究的分辨率，促进准确的物种/基因型鉴别，并加速具有增强生物和非生物耐受性的转基因植物的开发。
在线版本包含可在10.1007/s13205-021-02943-0获取的补充材料。
