Summary: Gene duplication occurs via different modes such as segmental and single-gene duplications. Transposed gene duplication, a specific form of single-gene duplication, ‘copies’ a gene from an ancestral chromosomal location to a novel location. MCScanX is a toolkit for detection and evolutionary analysis of gene colinearity. We have developed MCScanX-transposed, a software package to detect transposed gene duplications that occurred within different epochs, based on execution of MCScanX within and between related genomes. MCScanX-transposed can be also used for integrative analysis of gene duplication modes for a genome and to annotate a gene family of interest with gene duplication modes. Availability:MCScanX-transposed is freely available at http://chibba.pgml.uga.edu/mcscan2/transposed/. Contact:wyp1125@gmail.com or paterson@plantbio.uga.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Epistatic interactions of multiple single nucleotide polymorphisms (SNPs) are now believed to affect individual susceptibility to common diseases. The detection of such interactions, however, is a challenging task in large scale association studies. Ant colony optimization (ACO) algorithms have been shown to be useful in detecting epistatic interactions.

Background: Divergence in gene structure following gene duplication is not well understood. Gene duplication can occur via whole-genome duplication (WGD) and single-gene duplications including tandem, proximal and transposed duplications. Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence. Results: In Arabidopsis thaliana, we denote levels of structural divergence between duplicated genes by differences in coding-region lengths and average exon lengths, and the number of insertions/deletions (indels) and maximum indel length in their protein sequence alignment. Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure. In transposed duplications, parental loci tend to have longer coding-regions and exons, and smaller numbers of indels and maximum indel lengths than transposed loci, reflecting biased structural changes in transposed duplications. Structural divergence increases with evolutionary time for WGDs, but not transposed duplications, possibly because of biased gene losses following transposed duplications. Structural divergence has heterogeneous relationships with nucleotide substitution rates, but is consistently positively correlated with gene expression divergence. The NBS-LRR gene family shows higher-than-average levels of structural divergence. Conclusions: Our study suggests that structural divergence between duplicated genes is greatly affected by the mechanisms of gene duplication and may be not proportional to evolutionary time, and that certain gene families are under selection on rapid evolution of gene structure.

Summary: Whole‐genome duplication (WGD) has been recurring and single‐gene duplication is also widespread in angiosperms. Recent whole‐genome DNA methylation maps indicate that gene body methylation (i.e. of coding regions) has a functional role. However, whether gene body methylation is related to gene origins and duplication modes has yet to be reported. In rice (Oryza sativa), we computed a body methylation level (proportion of methylated CpG within coding regions) for each gene in five tissues. Body methylation levels follow a bimodal distribution, but show distinct patterns associated with transposable element‐related genes; WGD, tandem, proximal and transposed duplicates; and singleton genes. For pairs of duplicated genes, divergence in body methylation levels increases with physical distance and synonymous (Ks) substitution rates, and WGDs show lower divergence than single‐gene duplications of similar Ks levels. Intermediate body methylation tends to be associated with high levels of gene expression, whereas heavy body methylation is associated with lower levels of gene expression. The biological trends revealed here are consistent across five rice tissues, indicating that genes of different origins and duplication modes have distinct body methylation patterns, and body methylation has a heterogeneous relationship with gene expression and may be related to survivorship of duplicated genes.