Identifying gene clusters within localized regions in multiple genomes

Discovering patterns in gene order

Various genetic events during the process of natural evolution shape the landscape of the genomes. In this chapter, we explore an approach to investigating multiple genomes in order to unravel their complex relationships that go beyond their placement on a phylogeny. To this end, we treat genes as the smallest syntactic unit on the genome and explore their relative organization across multiple genomes. In the first half of the chapter, we discuss mathematical models to capture the combinatorial structures of this relative organization and statistical models to study their distributions. In the second half of the chapter, we apply these models to analyze the relationship between three closely related plant genomes.

Identification of conserved gene clusters in multiple genomes based on synteny and homology

Background

Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.

Results

Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.

Conclusions

The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.