Sequencing hundreds of genes in sunflower family now possible
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 included, and around 700 of these genes were determined to be orthologous and thus suitable for phylogenetic analysis. Using these orthologous genes, they were able to generate well-resolved phylogenetic trees consistent with known relationships in the family, demonstrating the successfulness of this approach for phylogenetic studies of the Compositae.
Although the probe set was developed specifically for research on the sunflower family, the researchers note that the overall workflow can be applied to any taxonomic group of interest. Therefore, this protocol could serve as a model for phylogenetic investigations of other major plant groups, as well as an excellent tool for studies of the Compositae.
"Novel probes can be designed as long as transcriptomic data exists or can be gathered for the taxa of interest," says Mandel.
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