According to Jennifer Mandel, assistant professor in the Department of Biological Sciences at University of Memphis and lead author of the paper, the new approach is an improvement on traditional, PCR-based sequencing strategies, which have generally focused on chloroplast genes or a handful of nuclear genes. "Our method samples the genome much more widely, while avoiding the repetitive regions that make many plant genomes so difficult to assemble," says Mandel.
The protocol employs custom-designed probes that can hybridize with and "capture" 1061 nuclear genes from DNA samples of sunflower species. The captured genes can then be sequenced on the Illumina HiSeq or a similar next-generation sequencing platform, allowing tremendous amounts of data to be recovered for phylogenetic analysis.
The researchers also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting sequence data. The workflow assembles the genes from the millions of reads generated from the sequencing instrument and then assesses all of the recovered genes for orthology (i.e., for their ability to reflect speciation events and, therefore, to accurately reconstruct phylogenetic relationships). The genes that pass the orthology test are then used for large-scale phylogenetic analyses.
The researchers tested the efficacy of the probes and overall workflow using 14 species from the family (and one from its closest relative, Calyceraceae). The species selected span the phylogenetic breadth of the family, allowing the researchers to assess the utility of the method at broad taxonomic levels. Several closely related species (from the tribe Heliantheae) were also included to assess the usefulness of the method for shallow phylogenetic studies within the Compositae.
The researchers were able to successfully recover a large portion of the 1061 target genes across all the species includ
|Contact: Beth Parada|
American Journal of Botany