Rice Genetics IV - IRRI books - International Rice Research Institute

Multiple gene trees: new insights into the phylogeny of OryzaRecent advances in phylogenetic methodologies together with the availability of newtypes of data have significantly increased the accuracy of phylogenetic reconstruction(Donoghue 1994). In particular, the phylogenetic utility of sequences of low-copynuclear genes has allowed us to address phylogenetic questions that were previouslychallenging. Low-copy nuclear genes, which contain fast-evolving introns and areless susceptible to concerted evolution, are especially powerful markers for reconstructingallopolyploidization at the interspecific level (Sang and Zhang 1999). Cautionhas to be exercised, however, when we infer a species tree from gene trees becausegene trees may not represent species trees when factors such as paralogy (referringto the common ancestry of the sequences originated from a gene duplicationevent), hybridization, or lineage sorting are involved. Therefore, it is an increasinglywidespread practice to apply multiple data sets to a common group of taxa (Wendeland Doyle 1998). Congruence among the multiple gene phylogenies provides a soundfoundation for a robust reconstruction of phylogenetic relationships of the organismsthemselves (Hillis and Huelsenbeck 1995).Recently, we have sequenced two nuclear genes, Adh1 and Adh2, and a chloroplastgene, matK, by PCR-amplifying and cloning of DNA from 23 Oryza species. Bycomparing Adh1 and Adh2 trees and the matK tree of the Oryza species, a new genometype (HK) was identified for the tetraploid O. schlechteri, the only Oryza specieswith an unknown genome type. The origin of the allotetraploid species was reconstructedbased on the Adh gene phylogenies with their maternal parents identifiedby the matK phylogeny. In addition, phylogenetic relationships of the rice genomesand species were reconstructed based on the three gene phylogenies (Figs. 1, 2, 3; Geet al 1999).The origin of allotetraploid speciesCytogenetic studies have shown that all the polyploid Oryza species are allotetraploids(2n=4x=28) that make up more than one-third of the species in the genus(Vaughan 1994). The formation of so many allotetraploids obscured the morphologicaldistinction between some diploid species, and consequently made Oryza a taxonomicallyand phylogenetically difficult group (Vaughan 1989).Phylogenetic analysis of single or low-copy nuclear gene sequences offers a newand effective way to study the evolution of allopolyploids (Gaut and Doebley 1997,Small et al 1998, Sang and Zhang 1999). An allotetraploid, originated through hybridizationof two diverged diploid species, includes two distinct diploid genomes.Homeologous loci contributed by diploid parents can be cloned and sequenced froman allotetraploid species. Analysis of these sequences together with the gene sequencesof the putative diploid parents enables us to unravel the pattern of hybrid speciation.Furthermore, since the chloroplast genome is maternally inherited in rice, analysis ofthe chloroplast matK gene offers an opportunity to identify the maternal parents ofallotetraploid species.Phylogeny of the genus Oryza . . . 95