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Nakatani Y, McLysaght A. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. Bioinformatics 2018; 33:i369-i378. [PMID: 28881993 PMCID: PMC5870716 DOI: 10.1093/bioinformatics/btx259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Motivation It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Results Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. Conclusions We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. Availability and implementation The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoichiro Nakatani
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
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Abstract
Some genomes are known to have incurred a genome doubling (tetraploidization) event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to “halve” the genome, i.e. to reconstruct the ancestral genome at the moment of tetraploidization, but the solution is often highly non-unique. To resolve this problem, we adapt the genome halving algorithm of El-Mabrouk and Sankoff to take account of an external reference genome. We apply this to reconstruct the tetraploid ancestor of maize, using either rice or sorghum as the reference.
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Affiliation(s)
- Chunfang Zheng
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Qian Zhu
- Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
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Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinformatics 2016; 17:400. [PMID: 27687569 PMCID: PMC5043639 DOI: 10.1186/s12859-016-1258-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 09/13/2016] [Indexed: 12/02/2022] Open
Abstract
Background The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models. However, it has been observed that genomes are highly plastic, and that whole regions can be moved, removed or duplicated in bulk. These structural variants (SV) have been shown to have significant impact on phenotype, but their study has been held back by the combinatorial complexity of the underlying models. Results We describe here a general model of structural variation that encompasses both balanced rearrangements and arbitrary copy-number variants (CNV). Conclusions In this model, we show that the space of possible evolutionary histories that explain the structural differences between any two genomes can be sampled ergodically.
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Affiliation(s)
- Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK. .,Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.
| | - Tracy Ballinger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.,Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA
| | - Benedict Paten
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA
| | - Glenn Hickey
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA
| | - David Haussler
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA
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Moret BME, Lin Y, Tang J. Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Abstract
BACKGROUND Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant proportion of segmental duplications in Mammals, and the Drosophila species group, to breakpoints in rearrangement events. RESULTS In this paper, we introduce and study a combinatorial problem, inspired from the breakpoint-duplication phenomenon, called the Genome Dedoubling Problem. It consists of finding a minimum length rearrangement scenario required to transform a genome with duplicated segments into a non-duplicated genome such that duplications are caused by rearrangement breakpoints. We show that the problem, in the Double-Cut-and-Join (DCJ) and the reversal rearrangement models, can be reduced to an APX-complete problem, and we provide algorithms for the Genome Dedoubling Problem with 2-approximable parts. We apply the methods for the reconstruction of a non-duplicated ancestor of Drosophila yakuba. CONCLUSIONS We present the Genome Dedoubling Problem, and describe two algorithms solving the problem in the DCJ model, and the reversal model. The usefulness of the problems and the methods are showed through an application to real Drosophila data.
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Abstract
Background Finding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well - most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions, especially if the duplicated or deleted segments are of arbitrary size. Results We recently proposed a heuristic algorithm for sorting unichromosomal genomes by reversals, block interchanges, tandem duplications, and deletions. In this paper, we extend this approach to multichromosomal genomes. We are now able to sort a multichromosomal ancestral genome into a genome of a descendant by a large set of different operations, including tandem duplications and deletions of segments of arbitrary size. Conclusion Experimental results show that our algorithm finds sorting sequences that have a weight close to the true evolutionary distance.
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Affiliation(s)
- Martin Bader
- Institute of Theoretical Computer Science, Ulm University, 89069 Ulm, Germany.
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Abstract
BACKGROUND Finding sequences of evolutionary operations that transform one genome into another is a classic problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well--most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions. Almost all of these algorithms restrict these operations to have a fixed size. RESULTS In this paper, we present a heuristic algorithm to sort an ancestral genome (with unique gene content) into a genome of a descendant (with arbitrary gene content) by reversals, block interchanges, tandem duplications, and deletions, where tandem duplications and deletions are of arbitrary size. CONCLUSION Experimental results show that our algorithm finds sorting sequences that are close to an optimal sorting sequence when the ancestor and the descendant are closely related. The quality of the results decreases when the genomes get more diverged or the genome size increases. Nevertheless, the calculated distances give a good approximation of the true evolutionary distances.
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Affiliation(s)
- Martin Bader
- Institute of Theoretical Computer Science, University of Ulm, 89069 Ulm, Germany.
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Alekseyev MA, Pevzner PA. Colored de Bruijn graphs and the genome halving problem. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2007; 4:98-107. [PMID: 17277417 DOI: 10.1109/tcbb.2007.1002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based on generalized breakpoint graphs. The generalized breakpoint graphs make the El-Mabrouk-Sankoff result more transparent and promise to be useful in future studies of genome rearrangements.
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Affiliation(s)
- Max A Alekseyev
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla 92093-0114, USA.
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Abstract
MOTIVATION Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes. RESULTS In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.
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Affiliation(s)
- Peng Yin
- Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA.
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Abstract
Comparing chromosomal gene order in two or more related species is an important approach to studying the forces that guide genome organization and evolution. Linked clusters of similar genes found in related genomes are often used to support arguments of evolutionary relatedness or functional selection. However, as the gene order and the gene complement of sister genomes diverge progressively due to large scale rearrangements, horizontal gene transfer, gene duplication and gene loss, it becomes increasingly difficult to determine whether observed similarities in local genomic structure are indeed remnants of common ancestral gene order, or are merely coincidences. A rigorous comparative genomics requires principled methods for distinguishing chance commonalities, within or between genomes, from genuine historical or functional relationships. In this paper, we construct tests for significant groupings against null hypotheses of random gene order, taking incomplete clusters, multiple genomes, and gene families into account. We consider both the significance of individual clusters of prespecified genes and the overall degree of clustering in whole genomes.
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Affiliation(s)
- Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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Abstract
Comparative maps record the history of chromosome rearrangements that have occurred during the evolution of plants and animals. Effective use of these maps in genetic and evolutionary studies relies on quantitative analyses of the patterns of segment conservation. We review the analytical methods that have been developed for characterizing these maps and evaluate their application to existing comparative maps mainly for plants and animals.
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Affiliation(s)
- J H Nadeau
- Genetics Department, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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