Coordinate systems for supergenomes

Abstract

BackgroundGenome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting comparative, evolutionary analysis is also growing. In particular, efficient tools to visualize-omics data simultaneously for multiple species are sorely lacking. A first and crucial step in this direction is the construction of a common coordinate system. Since genomes not only differ by rearrangements but also by large insertions, deletions, and duplications, the use of a single reference genome is insufficient, in particular when the number of species becomes large.ResultsThe computational problem then becomes to determine an order and orientations of optimal local alignments that are as co-linear as possible with all the genome sequences. We first review the most prominent approaches to model the problem formally and then proceed to showing that it can be phrased as a particular variant of the Betweenness Problem. It is NP hard in general. As exact solutions are beyond reach for the problem sizes of practical interest, we introduce a collection of heuristic simplifiers to resolve ordering conflicts.ConclusionBenchmarks on real-life data ranging from bacterial to fly genomes demonstrate the feasibility of computing good common coordinate systems.Electronic supplementary materialThe online version of this article (10.1186/s13015-018-0133-4) contains supplementary material, which is available to authorized users.

Superbubbles revisited

“…All computations were performed on a 2.5GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7GHz) with 6MB shared L3 cache and 16GB of 1600MHz DDR3L onboard memory. Test data sets are taken from [4] and from the Stanford Large Network Dataset Collection [21]. The table lists their number N of vertices, M of edges and S of superbubbles…”

“…[3]. Superbubbles also appear naturally in the multigraphs in the context of supergenome coordinatization [4], i.e., the problem of finding good common coordinate systems for multiple genomes.…”

SMORE: Synteny Modulator of Repetitive Elements

“…This creates artefacts, because the initial alignment step by construction cannot distinguish between the individual copies of a family of loci that is subject to concerted evolution. We refer to [ 23 , 52 ] for a more extensive discussion of this issue. For mammals, we used the MultiZ alignment of 19 mammalian genomes with humans [ 53 ] and for nematodes, and the MultiZ alignment of 25 nematode genomes with Caenorhabditis elegans [ 54 ], downloadable through the University of California Santa Cruz (UCSC) Genome Browser.…”

Direct Superbubble Detection

“…All computations were performed on a 2.5-GHz quad-core Intel Core i7 processor (Turbo Boost up to 3.7 GHz) with 6-MB shared L3 cache and 16 GB of 1600-MHz DDR3L onboard memory. Test datasets were taken from [11] and from the Stanford Large Network Dataset Collection [12]. For each test graph, we list the number of vertices N, the numbers of edges M, and the number S of superbubbles.…”