The Papaya-DB will also allow for inter-taxon comparisons using Arabidopsis or the papaya genome as reference points. For this purpose, an external link to PGDD (Plant Genome Duplication Database Database) provides whole-genome alignments of papaya to grape, poplar, Arabidopsis, and other genome sequences, using a multialignment algorithm (Tang et al., 2008; Tang et al., in press). PGDD is a web-based database that displays the multiple alignments across several sequenced plant genomes. The alignments are generated by a robust computer program MCscan (Tang et al., in press). MCscan is capable of simultaneously scanning the collinearity patterns among multiple genomes and subgenomes to identify homologous chromosomal regions and subsequently aligning these regions using matching gene as anchors. Such comparisons are essential to understanding the course of plant genome evolution in the context of recurring polyploidies (Tang et al., 2008).

References:

Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M. and Paterson, A.H. (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps, Genome Research, in press.

Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M. and Paterson, A.H. (2008) Synteny and Collinearity in Plant Genomes, Science, 320, 486-488.