Restriction Site Variation in the Chloroplast Genome of Sorghum (Poaceae)

Restriction site variation was analyzed in the chloroplast (cp) DNA's of six species of Sorghum and one species each of Cleistachne and Zea. Each cpDNA was separately digested with 14 restriction enzymes and hybridized with six maize or sorghum cpDNA probes that together comprise approximately 75% of the plastid genome. Eighty-four restriction site mutations and two deletion mutations were observed among the cpDNA's of these species. These variable character mutations were used in phylogenetic analyses to construct rooted, most-parsimonious, phylogenetic trees on which confidence limits were placed by bootstrap analysis. The estimated number of nucleotide substitutions per site between each of the cpDNA's was also calculated. These analyses 1) reveal a relatively high level of sequence divergence within the genus Sorghum relative to that of other genera; 2) confirm that Sorghum sect. Sorghum is a monophyletic group; 3) cast doubt on the monophyly of sect. Parasorghum; and 4) suggest that the genus Sorghum may be either para- phyletic or polyphyletic. The fact that restriction site presence/absence in the plastid genome could be easily studied between genera as divergent as Zea and Sorghum suggests that analysis of variation in cpDNA could be used to construct a phylogeny for the entire tribe Andropogoneae.