title: Patterns of selective constraints in noncoding DNA of rice.
abstract: BACKGROUND
  Several studies have investigated the relationships between selective constraints in introns and their length, GC content and location within genes. To date, however, no such investigation has been done in plants. Studies of selective constraints in noncoding DNA have generally involved interspecific comparisons, under the assumption of the same selective pressures acting in each lineage. Such comparisons are limited to cases in which the noncoding sequences are not too strongly diverged so that reliable sequence alignments can be obtained. Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice (O. sativa).
  
  
  RESULTS
  Our principal findings are: (1) intronic divergence is negatively correlated with intron length, a pattern that has previously been described in Drosophila and mammals; (2) there is a signature of strong purifying selection at splice control sites; (3) first introns are significantly longer and have a higher GC content than other introns; (4) the divergences of first and non-first introns are not significantly different from one another, a pattern that differs from Drosophila and mammals; and (5) short introns are more diverged than four-fold degenerate sites suggesting that selection reduces divergence at four-fold sites.
  
  
  CONCLUSIONS
  Our observation of stronger selective constraints in long introns suggests that functional elements subject to purifying selection may be concentrated within long introns. Our results are consistent with the presence of strong purifying selection at splicing control sites. Selective constraints are not significantly stronger in first introns of rice, as they are in other species.
authors.affiliation: Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China. bioinplant@zju.edu.cn
authors.forename: Xingyi
authors.initials: X
authors.lastname: Guo
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Peter D
authors.initials: PD
authors.lastname: Keightley
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D007438:Introns; D012275:Oryza / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant; D022821:RNA Splice Sites