Abstract
To determine the phylogenetic relationship between sugarcane cultivars and other members of the Saccharinae subtribe, we identified the fast evolving ITS1-5.8S-ITS2 (ITS = internal transcribed spacer; 5.8S = 5.8S ribosomal DNA) region of the sugarcane genome in the Sugarcane Expressed Sequence Tag (SUCEST) genome project database. Parsimony analysis utilizing this region and homologs belonging to the 23 closely related Andropogoneae currently deposited in the GenBank database has shown sugarcane as the sister group of Saccharum sinense. However, because there are few parsimony-informative characters and high homoplasy in the ITS1-5.8S-ITS2 region we were not able to determine with confidence the phylogenetic relationship between sugarcane and some of the remaining members of Saccharine subtribe. To find alternatives for the phylogenetic reconstruction of sugarcane evolutionary history, we selected 17 markers (nuclear, chloroplastic or mitochondrial) from the SUCEST database of which apha-tubulin, ribosomal protein L16 (rpl16) and DNA-directed RNA polymerase beta chain (rpoC2) were found to have a low incidence of polymorphism and comparable, or even faster, rates of evolution than the ITS1-5.8S-ITS2 region. We suggest that these markers should be considered as preferential choices for phylogenetic studies of Saccharinae subtribe.
Highlights
The Saccharum L. group is a polyploid complex within the Saccharinae subtribe of the Andropogoneae Dumort tribe which itself if located within the Poaceae family (Sobral et al, 1994; Jacobs and Everett, 2000)
The Sugarcane Expressed Sequence Tag (SUCEST) genome project is an outstanding source of information because it contains many of the genes expressed by sugarcane cultivars used in agriculture
We identified sugarcane internal transcribed spacer (ITS) ITS1 and ITS2 sequences and used them to infer the phylogenetic position of sugarcane within the Saccharinae
Summary
The Saccharum L. group is a polyploid complex within the Saccharinae subtribe of the Andropogoneae Dumort tribe which itself if located within the Poaceae family (Sobral et al, 1994; Jacobs and Everett, 2000). The molecular systematics of the Andropogoneae would greatly benefit from markers with similar, or even faster, rates of evolution compared to that of the ITS regions. In this regard, the Sugarcane Expressed Sequence Tag (SUCEST) genome project is an outstanding source of information because it contains many of the genes expressed by sugarcane cultivars used in agriculture. Our results indicate that at least three sugarcane markers have comparable or even faster evolution rates than the ITS regions and can be considered as preferential choices for use in research on the molecular systematics of the Saccharinae subtribe
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