Coevolution between nuclear and plastid genomes in Geraniaceae
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Plastid genomes of angiosperms are highly conserved in both genome organization and nucleotide substitution rates. Geraniaceae have highly rearranged genomes and elevated nucleotide substitution rates, which provides an attractive system to study nuclear-plastid genome coevolution. My dissertation research has focused on two areas of nuclear-plastid genome coevolution in Geraniaceae. First, I have investigated the correlation of nucleotide substitution rates between nuclear and plastid genes that encode interacting subunits that form the multi-subunit complex of Plastid Encoded RNA Polymerase (PEP). Second, the hypothesis that the unusual changes of plastid genome organization and elevated nucleotide substitution rates of plastid encoded genes is the result of alterations in nuclear encoded DNA replication, recombination and repair (DNA RRR) genes is tested. The second chapter investigates the optimal methods for transcriptome sequencing/assembly. My findings supported the use of transcriptome assemblers optimized for Illumina sequencing platform (Trinity and SOAPdenovo-trans). The third chapter investigated coevolution of nucleotide substitution rates between plastid encoded RNAP (rpoA, rpoB, rpoC1, rpoC2) and nuclear encoded SIG (sig1-6) genes that are part of the multi-subunit complex PEP. Using the transcriptomes of 27 Geraniales species I extracted the PEP genes and performed a systematic correlation test. I detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) between RNAP and SIG but no correlations were detected for the control genes, which provides a plausible explanation for the cause of plastome-genome incompatibility in Geraniaceae. The fourth chapter investigated the effect of DNA RRR system on the aberrant evolutionary phenomena in Geraniaceae plastid genomes. I extracted DNA RRR and nuclear control genes with different subcellular locations from 27 Geraniales transcriptomes and estimated genome complexity with various measures from plastid genomes of the same species. I detected significant correlations for dN but not dS for three DNA RRR genes, 10 nuclear encoded plastid targeted (NUCP) and three nuclear encoded mitochondrial targeted (NUMT) genes. The findings of a correlation between dN of DNA RRR genes and genome complexity support the hypothesis that changes of plastid genome complexity in Geraniaceae may be caused by dysfunction of DNA RRR systems.
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