De novo assembly of complete chloroplast genomes

Geneious provides all of the tools for performing rapid and accurate de novo assembly of chloroplast genomes from short-read Next-Generation Sequencing (NGS) data. The NGS data may be derived DNA extracted from purified... [ view full abstract ]

Geneious provides all of the tools for performing rapid and accurate de novo assembly of chloroplast genomes from short-read Next-Generation Sequencing (NGS) data. The NGS data may be derived DNA extracted from purified chloroplasts, or filtered from whole-genome sequence of total DNA derived from chloroplast-rich leaf material. Chloroplast genomes are typically 120,000-170,000 bp long and contain a substantial fraction of almost perfect inverted repeats (IR, 2 of ≈25,000 bp each). This means a complete circular plastome cannot be resolved during assembly using only single-end short-reads. However, paired-end reads data, combined with appropriate tools for identification of the repeat and truncated repeat boundaries, can allow reconstruction of the complete circular plastome.

Here we describe how to perform such analyses using Geneious. We reconstruct a complete circular chloroplast genome, using as input paired-end short-reads from Sesame indicum (SRR949054). The final genome draft was also fully annotated within Geneious, including the accurate identification of SNPs and IR units.