Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

Abstract

The synonymous substitution rate varies widely among species, but it is generally quite stable within a genome due to the absence of strong selective pressures. In plants, plastid genes tend to evolve faster than mitochondrial genes, rate variation among species generally correlates between the mitochondrial and plastid genomes, and few examples of intragenomic rate heterogeneity exist. To study the extent of substitution rate variation between and within plant organellar genomes, we sequenced the complete mitochondrial and plastid genomes from the bugleweed, Ajuga reptans, which was previously shown to exhibit rate heterogeneity for several mitochondrial genes. Substitution rates were accelerated specifically in the mitochondrial genome, which contrasts with correlated plastid and mitochondrial rate changes in most other angiosperms. Strikingly, we uncovered a 340-fold range of synonymous substitution rate variation among Ajuga mitochondrial genes. This is by far the largest amount of synonymous rate heterogeneity ever reported for a genome, but the evolutionary forces driving this phenomenon are unclear. Selective effects on synonymous sites in plant mitochondria are generally weak and thus unlikely to generate such unprecedented intragenomic rate heterogeneity. Quickly evolving genes are not clustered in the genome, arguing against localized hypermutation, although it is possible that they were clustered ancestrally given the high rate of genomic rearrangement in plant mitochondria. Mutagenic retroprocessing, involving error-prone reverse transcription and genomic integration of mature transcripts, is hypothesized as another potential explanation.

Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa

“…The overall A-T contents of two genomes are 62.0% which is similar with general angiosperms and other cp genomes of Lamiaceae and some genus of Orobanchaceae (Shinozaki et al 1986;Kim & Lee 2004;Yi & Kim 2012;Wicke et al 2013;Zhu et al 2014;Welch et al 2016). In both of two genomes, the A-T content in the non-coding (64.6%) is higher than in the coding (60.1%) regions.…”

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae

“…Draft organellar genomes of C. paramensis and B. pedicularioides were assembled from the Illumina sequence reads with Velvet version 1.2.0342 using multiple combinations of kmer (61, 71, 81, 91) and expected coverage (50, 100, 200, 500, 1000) values, as described previously4344. Organellar contigs were identified in each assembly by using default blastn searches with known organellar gene sequences from related Lamiales species as queries.…”

“…Using this strategy, circular-mapping plastid and mitochondrial genomes were assembled for C. paramensis , and a draft mitogenome was assembled for B. pedicularioides . The C. paramensis and B. pedicularioides mitogenome assemblies were annotated as described previously324445. The C. paramensis plastid genome was annotated using DOGMA46 followed by manual adjustment as necessary.…”

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

“…Mitochondria boast some of the highest (108) and lowest (104) mutation rate estimates from any eukaryotic or bacterial genome. For angiosperms alone there is a 5,000-fold range in the absolute rate of synonymous site substitutions (d S ) among explored mitochondrial genomes (104), and up to a 340-fold range among genes within a single mtDNA (109). The mitochondrial synonymous substitution rate range is almost as staggering for cnidarians (103), sponges (110), and other animals (111), as well as for various protists, including alveolates (112,113) and amoebozoans (114).…”