Abstract
MotivationComplete organellar genome sequences (chloroplasts and mitochondria) provide valuable resources and information for studying plant molecular ecology and evolution. As high-throughput sequencing technology advances, it becomes the norm that a shotgun approach is used to obtain complete genome sequences. Therefore, to assemble organellar sequences from the whole genome, shotgun reads are inevitable. However, associated techniques are often cumbersome, time-consuming, and difficult, because true organellar DNA is difficult to separate efficiently from nuclear copies, which have been transferred to the nucleus through the course of evolution.ResultsWe report a new, rapid procedure for plant chloroplast and mitochondrial genome sequencing and assembly using the Roche/454 GS FLX platform. Plant cells can contain multiple copies of the organellar genomes, and there is a significant correlation between the depth of sequence reads in contigs and the number of copies of the genome. Without isolating organellar DNA from the mixture of nuclear and organellar DNA for sequencing, we retrospectively extracted assembled contigs of either chloroplast or mitochondrial sequences from the whole genome shotgun data. Moreover, the contig connection graph property of Newbler (a platform-specific sequence assembler) ensures an efficient final assembly. Using this procedure, we assembled both chloroplast and mitochondrial genomes of a resurrection plant, Boea hygrometrica, with high fidelity. We also present information and a minimal sequence dataset as a reference for the assembly of other plant organellar genomes.
Highlights
Organellar genomes are widely used in evolutionary and population genetics studies
Plant cells can contain multiple copies of the organellar genomes, and there is a significant correlation between the depth of sequence reads in contigs and the number of copies of the genome
We present information and a minimal sequence dataset as a reference for the assembly of other plant organellar genomes
Summary
Organellar genomes are widely used in evolutionary and population genetics studies. The plastid genome contains many essential genes, especially those required for photosynthesis. Information from multiple plastid genomes harbors suites of characters that transcend the green plant branch in the tree of life [1]. There are multiple copies of the organellar genomes in plant cells, e.g. plant leaf cells often contain 400 to 1,600 copies of the plastid genome [2]. Most chloroplast (cp) genomes are circular DNA molecules ranging from 120 to 160 kb. They have a quadripartite organization, consisting of two copies of inverted repeats (IRs) of 2028 kb in size, which divides the rest of the genome into
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