Abstract
BackgroundCompared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change.Methodology/Principal FindingsWe determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses.Conclusions/SignificanceOur result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects.
Highlights
Next-generation sequencing that is high-throughput and low-cost has already revolutionized approaches for genome sequencing and is becoming ‘now-generation’ sequencing [1]
Since no estimated size existed for the F. rimosivaginus mt genome in previous studies, we evaluated the degree of sequence completion by comparing the assembly size to the average size (484,329 bp) of mt genomes from three closely related species B. oldhamii, Oryza sativa (NC_011033) [38] and Triticum aestivum (NC_007579) [39]
The rate change exhibited limit of variation between genes and the majority of ratios had a value around 5.00. Due to their high-throughput and low-cost, next-generation sequencing technologies have greatly improved the approaches for genome sequencing. They have been largely restricted to sequencing of cp genomes until now
Summary
Next-generation sequencing that is high-throughput and low-cost has already revolutionized approaches for genome sequencing and is becoming ‘now-generation’ sequencing [1]. The 21 available mt genomes of higher plants (Table 1) are essentially obtained by Sanger sequencing, involving extracting or PCR amplification of mtDNA and library construction prior to sequencing This timeand labour-intensive sequencing approach to some extent limits the sequencing of plant mt genomes. This would be a rapid and efficient approach to sequence angiosperm mt genomes and more sequenced genomes will be helpful in understanding the extraordinary evolutionary history of angiosperm mt genomes Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. Unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. A time-calibrated phylogenetic tree is needed to examine rate change
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