Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species

Abstract

Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.

Figure 1.

Distribution of features on japonica chromosome 3. The pseudomolecule was annotated for features including gene models, transcript evidence, repetitive sequences, tRNA genes, genetic markers, organellar insertions, and flanking sequence tags (FSTs). These are identified on the pseudomolecule using a false color display. Genetic markers are positioned at 10-cM intervals (approximately). Physical gaps are noted separately (black ticks) and include the gap at the centromere (red). Gene model density (GD) is noted in two separate tiles, all gene models and non-TE-related gene models. Expression density reflects gene models with transcript evidence. FST denotes the presence of a sequence-tagged insertion among tagged populations. Repetitive sequences are represented by the TE DNA and MITE tiles. tRNA genes and organellar insertions (CP/MT) are also denoted.

Figure 2.

Plot of insertion/deletion/null blocks relative to the O. nivara chromosome 3 FPC map using a 200-kb sliding window across the japonica chromosome 3 pseudomolecule. Percent difference (%D) between sizes from O. nivara paired BAC ends and high-resolution HindIII fingerprints was plotted using a 200-kb window across the japonica chromosome 3 pseudomolecule, where a >20% difference is red (insertion), -20%∼20% is purple (null), and <-20% is blue (deletion). Percentage difference was calculated using the following formula: {[(paired BES size) - (FP size)]/(FP size)} × 100. A percentage decrease (left) or increase (right) was plotted on the bar graph on either side of the consensus. Regions of the japonica chromosome 3 pseudomolecule that were not covered by O. nivara paired BAC end sequences are represented in gray.

Figure 3.

Syntenic relationship between japonica chromosome 3 and maize chromosomes 1, 5, and 9. We used maize markers, such as anchored markers and EST-derived overgoes and BAC end sequences to construct this syntenic map with the rice chromosome 3 pseudomolecule. Graphics were generated using SyMAP (www.agcol.arizona.edu/symap). (A) Overall picture of the rice chromosome 3-maize synteny. Rice chr3: the filled black bar; maize chr1 (red), chr5 (orange), and chr9 (blue). (B) Synteny of rice chromosome 3 pseudomolecule to the maize FPC map. (C,D) Synteny of the short arm of rice chromosome 3 with maize chromosomes 1 and 9 in detail. (E,F) Synteny of the long arm of rice chromosome 3 with maize chromosomes 1 and 5 in detail. (Green line) Marker and overgoes-originated EST sequences; (purple line) maize BAC end sequences.