Cassis: detection of genomic rearrangement breakpoints

Baudet, Christian; Lemaitre, Claire; Dias, Zanoni; Gautier, Christian; Tannier, Éric; Sagot, Marie‐France

doi:10.1093/bioinformatics/btq301

Cited by 24 publications

(29 citation statements)

References 4 publications

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“…Due to alignment and SF detection settings, some of the intervals between adjacent SFs could be >6 kb, and primers could not be chosen for a reliable PCR amplification. In such cases, we used CASSIS software (Baudet et al 2010) and the underlying alignment results to narrow gaps between adjacent SFs where possible. Whole blood was collected aseptically from adult falcons and pigeons.…”

Section: Pcr Testing Of Adjacent Sfsmentioning

confidence: 99%

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

et al. 2016

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Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.

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Section: Pcr Testing Of Adjacent Sfsmentioning

confidence: 99%

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

et al. 2016

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“…1). A variety of comparative genomics tools have been designed to perform this analysis (e.g., Baudet et al 2010;Skovgaard et al 2011). In the second stage, summary statistics should be designed and computed at the local level (for each genomic region) and at the global level (whole genome) (see Fig.…”

mentioning

confidence: 99%

Advances in Computer Simulation of Genome Evolution: Toward More Realistic Evolutionary Genomics Analysis by Approximate Bayesian Computation

Arenas

2015

J Mol Evol

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NGS technologies present a fast and cheap generation of genomic data. Nevertheless, ancestral genome inference is not so straightforward due to complex evolutionary processes acting on this material such as inversions, translocations, and other genome rearrangements that, in addition to their implicit complexity, can co-occur and confound ancestral inferences. Recently, models of genome evolution that accommodate such complex genomic events are emerging. This letter explores these novel evolutionary models and proposes their incorporation into robust statistical approaches based on computer simulations, such as approximate Bayesian computation, that may produce a more realistic evolutionary analysis of genomic data. Advantages and pitfalls in using these analytical methods are discussed. Potential applications of these ancestral genomic inferences are also pointed out.

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“…Thus we ran the Cassis software [2] to identify 38 breakpoints on the chimp genome during the period of evolutionary divergence from humans.…”

Section: Breakpoints For the Cerebral Cortex Studymentioning

confidence: 99%

“…This is not a trivial exercise. There are now high-resolution techniques to identify breakpoint regions [12,13,2], and thousands of data sets containing the results of whole-genome microarray assays, but comparative, whole genome data sets, controlled for tissue, with orthologous chromosomal positions specified for two species, are not easy to come by [14].…”

Section: Introductionmentioning

confidence: 99%

Changes in gene expression near evolutionary breakpoints

Muñoz

Sankoff

2011

Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine

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We study the relation between genome rearrangements, breakpoints and gene expression. Genome rearrangement research has been concerned with the creation of breakpoints and their position in the chromosome, but the functional consequences of individual breakpoints remain virtually unknown, and there are no direct genome-wide studies of breakpoints from this point of view. A question arises of what the biological consequences of breakpoint creation are, rather than just their structural aspects. The question is whether proximity to the site of a breakpoint event changes the activity of a gene. We investigate this by comparing the distribution of distances to the nearest breakpoint of genes that are differentially expressed with the distribution of the same distances for the entire gene complement. We study this in data on whole blood tissue in human versus macaque, and in cerebral cortex tissue in human versus chimpanzee. We find in both data sets that the distribution of distances to the nearest breakpoint of "changed expression genes" differs little from this distance calculated for the rest of the gene complement. In focusing on the changed expression genes closest to the breakpoints, however, we discover that several of these have previously been implicated in the literature as being connected to the evolutionary divergence of humans from other primates.

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Cassis: detection of genomic rearrangement breakpoints

Cited by 24 publications

References 4 publications

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

Advances in Computer Simulation of Genome Evolution: Toward More Realistic Evolutionary Genomics Analysis by Approximate Bayesian Computation

Changes in gene expression near evolutionary breakpoints

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