Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

Abstract

BackgroundThe identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies.ResultsIn this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach.ConclusionWe apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes.

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

“…The expected number of occurrences of a pairwise collinearity pattern could be estimated with the following, similar to the one used in Wang et al (2006),…”

“…The expectation multiplies by two since there are two possible orientation configurations between two collinear segments. This is only an approximation to a more rigorous yet computationally expensive permutation test (Van de Peer 2004) and Monte Carlo methods (Hampson et al 2005); however, computational experiments and analytical results (Wang et al 2006) suggest that this gives a reasonable estimate for the significance of the syntenic blocks. All the pairwise alignments that we reported are significant at E < 1 ‫ן‬ 10…”

“…Continuous stretches of duplicate genes can be computationally deduced through synteny, using some variants of clustering approaches (Vandepoele et al 2002;Hampson et al 2005) or more specifically using dynamic programming with a customized scoring scheme if conserved gene order (collinearity) is also considered (Haas et al 2004;Wang et al 2006). Traditional methods for deduction of synteny based on "best-in-genome" criteria (Miller et al 2007), uncovering one-to-one best matching regions during pairwise genome comparisons, are relatively straightforward in vertebrates yet difficult in angiosperms because of additional challenges that are more prominent in angiosperm genomes (Tang et al 2008).…”

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

“…A built-in scoring scheme for MCscan is min(Àlog 10 E_value, 50) for every matching gene pair and À1 for each 10 Kb distance between anchors and blocks that have scores >300 were kept. The resulting syntenic chains are evaluated using a procedure by ColinearScan (Wang et al 2006).…”

Polyploidy-associated genome modifications during land plant evolution

“…Another method to detect synteny is to employ dynamic programming to find the highest scoring 'chains' of syntenic genes, performing empirical or statistical tests to determine whether the observed synteny could have arisen by chance as implemented in DAGchainer [64], ColinearScan [65], MCscan [58] and MCscanX [61]. In addition, several web-based systems have been developed for wholegenome analysis.…”