ARS | Publication request: Phylogenetic analysis of Rutaceous plants based on single nucleotide polymorphism in chloroplast and nuclear gene sequences

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2008
Publication Date: N/A

Technical Abstract: The family Rutaceae encompasses several genera including the economically important genus Citrus. In this study, we selected 22 citrus relatives belonging to the various sub groups of Rutaceae and compared the sequences of three gene fragments. The accessions selected belong to the subfamily Rutoideae (Zanthoxylon), Toddalioideae (Casimiros) and subfamily Aurantioideae. Several members of Aurantioideae belonging to the subgroups Balsamocitrinae (Aegle), Citrinae (Citrus), Triphasinae (Pamburus) and Clauseneae (Murraya) were included in the study. The gene fragments studied included a nuclear house-keeping gene, malate dehydrogenase, in addition to two chloroplast genes. The chloroplast gene fragments consisted of: a) an 850 bp non-coding intergenic region between atpB and rbcL genes and b) a 900 bp intron region of the ribosomal protein gene rps 16. The nuclear gene analyzed had both intron and exon regions. In all three genes, introns were rich in parsimony informative characters. Single nucleotide polymorphisms and indels were aligned, partitioned and used for phylogenetic studies using PAUP and Mr. Bayes analyses. The phylogenetic information generated provides a source of SNP markers and aids in a better understanding of the relationships between the different accessions studied.