Evaluating synteny for improved comparative studies

Abstract

Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected—what few results are given use superficial measures unrelated to quality or consistency.Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles.Contact: cristinagabriela.ghiurcuta@epfl.ch

Inferring synteny between genome assemblies: a systematic evaluation

“…An alternative and arguably more practical approach relies on the identification of synteny blocks [13, 14], first described as homologous genetic loci that co-occur on the same chromosome [15, 16]. Synteny blocks are more formally defined as regions of chromosomes between genomes that share a common order of homologous genes derived from a common ancestor [17, 18].…”

Similarity and dissimilarity of primary structures of some Streptomyces spp. genomes and the Streptomyces globisporus 1912-2 chromosomal DNA.

“…The presence of different assortments of addition genes (or gene clusters) and different location of homologous genes in chromosomes of such strains were indicated. However, there are certain models in the construction of chromosomes: for example, the same order of localization of homologous genes in similar clusters (synteny), the accumulation of obligatory genes in the central part of the chromosome [26].…”

Computational Synteny Block: A Framework to Identify Evolutionary Events

“…minimum SBs lengths, minimum number of blocks, nonoverlapped SBs, etc.). According to Ghiurcuta and Moret [12], the definition of SBs does not seem to be strict enough, which might explain why current tools yield widely different results. A comparative table on the different methods for computing SBs has been included in Supplementary Material, section 1.…”