Sequencing hundreds of genes in sunflower family now possible
Advances in DNA sequencing technologies have enormous potential for the plant sciences. With genome-scale data sets obtained from these new technologies, researchers are able to greatly improve our understanding of evolutionary relationships, which are key to applications including plant breeding and physiology.
Studies of evolutionary (or phylogenetic) relationships among different plant species have traditionally relied on analyses of a limited number of genes, mostly from the chloroplast genome. Such studies often fail to fully or accurately resolve phylogenetic relationships, given the limited amount of data used.
New methods of DNA sequencing have made it possible for researchers to sequence hundreds to thousands of specific nuclear genes, greatly facilitating studies of phylogenetic relationships. However, despite the great potential of this approach, termed "target sequence capture," few researchers have developed protocols to sequence numerous nuclear genes for plant phylogenetic studies.
Researchers at the University of Memphis, the Smithsonian Institution, the University of Georgia, and other institutions have designed an efficient approach for sequencing hundreds of nuclear genes across members of the Compositae (the sunflower family). The Compositae are one of the largest families of flowering plants, containing around 25,000 species and numerous economically important crop plants, such as lettuce, sunflower, and artichoke, as well as numerous ornamentals.
The new protocol (available for free viewing in the February issue of Applications in Plant Sciences) will allow researchers to better-resolve phylogenetic relationships at both deep and shallow levels within the family, providing an excellent framework for addressing evolutionary questions about the family. Previous phylogenetic studies of the family, based on up to 10 chloroplast genes, had failed to resolve certain key relationships, limiting inferences of morphological evolution.
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.
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