Evidence that rice, and other cereals, are ancient aneuploids.

Abstract

Detailed analyses of the genomes of several model organisms revealed that large-scale gene or even entire-genome duplications have played prominent roles in the evolutionary history of many eukaryotes. Recently, strong evidence has been presented that the genomic structure of the dicotyledonous model plant species Arabidopsis is the result of multiple rounds of entire-genome duplications. Here, we analyze the genome of the monocotyledonous model plant species rice, for which a draft of the genomic sequence was published recently. We show that a substantial fraction of all rice genes ( approximately 15%) are found in duplicated segments. Dating of these block duplications, their nonuniform distribution over the different rice chromosomes, and comparison with the duplication history of Arabidopsis suggest that rice is not an ancient polyploid, as suggested previously, but an ancient aneuploid that has experienced the duplication of one-or a large part of one-chromosome in its evolutionary past, approximately 70 million years ago. This date predates the divergence of most of the cereals, and relative dating by phylogenetic analysis shows that this duplication event is shared by most if not all of them.

Supplementary Data

• Genomic rice data
  A list of rice BAC sequences that was used to create the genomic scaffolds using ASGAR (Automatic Sequence-to-Genome Assembly Routine) and their position in the assembly, together with gene annotation can be found in this Excel file (26MB) or zipped Excel file (11MB). All genomic scaffolds (i.e. contigs and singleton BACs) used in this analysis with the corresponding RiceGAAS annotation mapped on it can be downloaded here (zipped tar of all files in EMBL format, 110 MB). A multiple fasta file of all rice proteins is available in gzip format (rice).

• Browse non-hidden duplicated segments
  Non-hidden duplications are duplicated segments that still show conserved colinearity, i.e. conserved gene content and order. All non-hidden block duplications can be browsed here. Chromosome numbers can be extracted from the list names (e.g. "CC08R2_14_final" is a genomic scaffold on chromosome 8).

• Browse multiplicons
  A multiplicon is a set of homologous segments, whereas the multiplication level is the number of homologous segments within the multiplicon. Here, multiplicons with segments of both Arabidopsis and rice can be viewed.

• Browse phylogenetic trees
  For all anchorpoints within duplicated segments, a phylogenetic tree was created if an dicot outgroup and monocot homologous could be find. All trees with their link to the corresponding non-hidden duplication can be viewed here.