Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

Abstract

Background: Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences.

Results: A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'.

Conclusion: Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.

Figure 1

Partial angiosperm taxonomy illustrating the relationship between monocot and dicot species included in the present analysis. Numbers represent estimated times of lineage divergences (million years before the present) relative to rice taken from ¹Bell et al. (2005) [26] and ²Gaut (2002) [58]. Taxonomic relationships were obtained from the NCBI Taxonomy browser [59].

Figure 2

Distribution of differently-annotated TIGR rice loci on rice pseudomolecules. Linear order of differently annotated types of TIGR rice loci (TRL) on each of the rice pseudomolecules (1–12) in relation to significant MegaBLAST sequence alignments between the Os_CD database and the test databases. For each rice pseudomolecule: column 1 (red) = combined test database significant alignments; column 2 (blue) = functionally annotated TRL or expressed protein, column 3 (blue) = hypothetical protein, column 4 (blue) = retro/transposon-related sequence. Pseudomolecules are aligned along the centromere (horizontal black bar).

Figure 3

Heat maps for % sequence alignments and average scores. Colour coded moving windows/100 functionally annotated, expressed TIGR rice loci (MWs/FAexpTRL) for each rice pseudomolecule (1–12). For each pseudomolecule: column 1–6 = MWs for % significant MegaBLAST alignments between Os_CD and test databases Lp_MF, Zm_MF, Zm_TA, Hv_TA, Gm_TA and At_TA respectively; column 7 = position of MWs containing rice centromere (dark vertical bar); column 8–13 = MWs for average score of significant MegaBLAST alignments between Os_CD and test databases Lp_MF, Zm_MF, Zm_TA, Hv_TA, Gm_TA and At_TA, respectively [see Additional file 2 Table 3 for colour code quantification]. Pseudomolecule representations are aligned along the centromeres.

Figure 4

Heat maps for % sequence alignments and segmentally duplicated rice loci. Colour coded moving windows/100 functionally annotated, expressed TIGR rice loci (MWs/FAexpTRL) for each rice pseudomolecule (1–12). For each pseudomolecule: column 1–6 = MWs for % significant MegaBLAST alignments between Os_CD and test databases Lp_MF, Zm_MF, Zm_TA, Hv_TA, Gm_TA and AT_TA, respectively; column 7 = position of MWs containing rice centromere (dark vertical bar); column 8 = MWs indicating the distribution of segmentally duplicated FAexpTRL [see Additional file 2 Table 3 for colour code quantification].