Molecular Evolutionary and Functional Genomic Studies of Marshallia (Asteraceae) Utilizing Next Generation Sequencing Technology

Abstract

Several aspects of Marshallia (Asteraceae) genomics have been investigated using NGS technologies. I have assembled and characterized Marshallia Clade III Cytokinin Response Factor genes from DNA and RNA datasets. To inform the assembly, over 50 Clade III CRF protein sequences from Asterid taxa were mined from public databases, aligned, and analyzed via MEME analyses. Two well-supported novel C-terminus motifs were identified. Expression experiments were conducted using Marshallia caespitosa to determine if the Marshallia Clade III CRF is upregulated by similar factors as Arabidopsis and Solanum Clade III CRF genes. Expression levels of the Marshallia Clade III CRF was only detectable after oxidative stress and cytokinin treatments, suggesting that it is expressed at very low basal levels. This gene was also found to be up-regulated by oxidative stress and by cytokinin treatment. I assembled, aligned, and compared the plastid genomes and transcriptomes for three species of Marshallia (M. mohrii, M. obovata, and M. trinervia) to identify plastid RNA editing sites. Thirty eight editing sites were identified, with 31 occurring in coding regions. Twenty four of the identified edit sites were found to occur in other taxa. Individuals of M. mohrii (a putative allopolyploid) exhibited decreased editing efficiency compared to diploid members of the genus included in this study. This work has extended knowledge of Clade III CRFs beyond model systems and characterized Plastid RNA editing in a non-model plant.