1
|
Abstract
Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.
Collapse
|
2
|
Greenman CD, Penso-Dolfin L, Wu T. The complexity of genome rearrangement combinatorics under the infinite sites model. J Theor Biol 2020; 501:110335. [DOI: 10.1016/j.jtbi.2020.110335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/16/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
|
3
|
Chauve C, El-Mabrouk N, Guéguen L, Semeria M, Tannier E. Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
4
|
Abstract
The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics, based on the representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy, and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss, and speciation), the cluster level (evolution by tandem duplications), and the genome level (all types of rearrangement events, including whole genome duplication).
Collapse
Affiliation(s)
- Nadia El-Mabrouk
- Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC, Canada
| | | |
Collapse
|
5
|
Tremblay Savard O, Bertrand D, El-Mabrouk N. Evolution of orthologous tandemly arrayed gene clusters. BMC Bioinformatics 2011; 12 Suppl 9:S2. [PMID: 22152029 PMCID: PMC3283317 DOI: 10.1186/1471-2105-12-s9-s2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in 1 makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted), deletions and inversion events. RESULTS We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. CONCLUSIONS Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. A limitation of the algorithm is however in dealing with multiple gene deletions, as the algorithm is highly exponential in this case, and becomes quickly intractable.
Collapse
Affiliation(s)
| | - Denis Bertrand
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore
| | - Nadia El-Mabrouk
- Department of Computer Science (DIRO), University of Montreal, Montreal, Quebec, Canada
| |
Collapse
|
6
|
Vinar T, Brejová B, Song G, Siepel A. Reconstructing histories of complex gene clusters on a phylogeny. J Comput Biol 2011; 17:1267-79. [PMID: 20874408 DOI: 10.1089/cmb.2010.0090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. These clusters are one of the major sources of evolutionary innovation, and they are linked to multiple diseases, including HIV and a variety of cancers. Understanding their evolutionary histories is a key to the application of comparative genomics methods in these regions of the genome. We propose a probabilistic model of gene cluster evolution on a phylogeny, and an MCMC algorithm for reconstruction of duplication histories from genomic sequences in multiple species. Several projects are underway to obtain high quality BAC-based assemblies of duplicated clusters in multiple species, and we anticipate use of our methods in their analysis.
Collapse
Affiliation(s)
- Tomás Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University , Bratislava, Slovakia
| | | | | | | |
Collapse
|
7
|
Kahn CL, Mozes S, Raphael BJ. Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol Biol 2010; 5:11. [PMID: 20047668 PMCID: PMC2820476 DOI: 10.1186/1748-7188-5-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 01/04/2010] [Indexed: 02/06/2023] Open
Abstract
Background Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally, we provide a description of a sequence of duplication events as a context-free grammar (CFG). Conclusion These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.
Collapse
|
8
|
Lajoie M, Bertrand D, El-Mabrouk N. Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Mol Biol Evol 2009; 27:761-72. [PMID: 19903657 DOI: 10.1093/molbev/msp271] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Gene duplication is frequent within gene clusters and plays a fundamental role in evolution by providing a source of new genetic material upon which natural selection can act. Although classical phylogenetic inference methods provide some insight into the evolutionary history of a gene cluster, they are not sufficient alone to differentiate single- from multiple gene duplication events and to answer other questions regarding the nature and size of evolutionary events. In this paper, we present an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions. We applied our algorithm to the human olfactory receptor and protocadherin gene clusters, showing that the duplication size distribution differs significantly between the two gene families. The algorithm is available through a web interface at http://www-lbit.iro.umontreal.ca/DILTAG/.
Collapse
Affiliation(s)
- Mathieu Lajoie
- Département d'informatique et de recherche opérationnelle Université de Montréal, Montréal, Canada.
| | | | | |
Collapse
|
9
|
Vinař T, Brejová B, Song G, Siepel A. Reconstructing Histories of Complex Gene Clusters on a Phylogeny. COMPARATIVE GENOMICS 2009. [DOI: 10.1007/978-3-642-04744-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
10
|
LaRue RS, Jónsson SR, Silverstein KAT, Lajoie M, Bertrand D, El-Mabrouk N, Hötzel I, Andrésdóttir V, Smith TPL, Harris RS. The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BMC Mol Biol 2008; 9:104. [PMID: 19017397 PMCID: PMC2612020 DOI: 10.1186/1471-2199-9-104] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 11/18/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND APOBEC3 (A3) proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3). The presence of one A3 gene in mice (Z2-Z3) and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3), suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs. RESULTS Sheep and cattle have three A3 genes, A3Z1, A3Z2 and A3Z3, whereas pigs only have two, A3Z2 and A3Z3. A comparison between domestic and wild pigs indicated that A3Z1 was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three A3 genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular A3 repertoire existed in the common ancestor of artiodactyls and primates (i.e., the ancestor of placental mammals). This mammalian ancestor therefore possessed the minimal A3 gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire. CONCLUSION The dynamic recombination-filled history of the mammalian A3 genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions) were selected by ancient pathogenic retrovirus infections.
Collapse
Affiliation(s)
- Rebecca S LaRue
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Beckman Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Stefán R Jónsson
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Beckman Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
- University of Iceland, Institute for Experimental Pathology, Keldur v/Vesturlandsveg, 112 Reykjavík, Iceland
| | - Kevin AT Silverstein
- Masonic Cancer Center, Biostatistics and Bioinformatics Group, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mathieu Lajoie
- DIRO, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
| | - Denis Bertrand
- DIRO, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
| | | | - Isidro Hötzel
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 99164-7040, USA
| | - Valgerdur Andrésdóttir
- University of Iceland, Institute for Experimental Pathology, Keldur v/Vesturlandsveg, 112 Reykjavík, Iceland
| | - Timothy PL Smith
- USDA/ARS US Meat Animal Research Center, Genetics and Breeding Research Unit, PO Box 166, Clay Center, Nebraska 68933-0166, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Beckman Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|