De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

Abstract

BackgroundSequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA.ResultsSequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome.ConclusionsThis study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

Comparative mitochondrial genome analysis of Pythium insidiosum and related oomycete species provides new insights into genetic variation and phylogenetic relationships

“…Three contigs (contig00001, contig00099, and contig00034), assembled from 26,927 reads (7.8 %), were revealed as parts of the mitochondrial genome by alignment with the mt genome of P. ultimum (Accession number: NC_014280). These three contigs were joined together to form a complete mitochondrial genome without gaps using contig graph (bb454Contig program) (Iorizzo et al, 2012). The resulting contig graph, presented in Figure 1A, shows that the contig00001 is duplicated as an inverted repeat (IR) region separated by the other two contigs.…”

“…Contigs with high sequencing coverage were considered as potentially derived from organellar genome sequences (Shearman et al, 2014;Tangphatsornruang et al, 2011). The mt genome sequence was constructed using the bb454Contig program (Iorizzo et al, 2012). Illumina HiSeq2000 paired-end sequence reads, generated from the same strain of P. insidiosum (Your Gene Bioscience, New Taipei City, Taiwan), were mapped to the draft mt genome to check for sequence accuracy, especially in the homopolymer regions, with Newbler Reference Mapper (seed = 12, identity > 90%).…”

Organellar genome analysis reveals endosymbiotic gene transfers in tomato

“…Gene transfer from mitochondria to plastids has been reported recently [36–40], but gene transfer from the nucleus to plastids appears to rarely occur [21]. Nuclear copies of mitochondrial DNA (NUMTs) as a result of endosymbiotic gene transfer (EGT) have been widely found from protists to animals [26].…”

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

“…Until recently, it was thought that plastids were impenetrable to foreign DNA (85,86). However, new data from various angiosperms uncovered mitochondrion-to-plastid (87,88) and nucleusto-plastid DNA migration events (89), and there are also examples of plastids, including those of some diatoms and the red alga Gracilaria tenuistipitata, acquiring genes from plasmid or bacterial genomes (69,90). Foreign DNA can also come in the form of extrachromosomal elements.…”