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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.
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Delabre M, El-Mabrouk N, Huber KT, Lafond M, Moulton V, Noutahi E, Castellanos MS. Evolution through segmental duplications and losses: a Super-Reconciliation approach. Algorithms Mol Biol 2020; 15:12. [PMID: 32508979 PMCID: PMC7249433 DOI: 10.1186/s13015-020-00171-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 05/05/2020] [Indexed: 02/02/2023] Open
Abstract
The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes.
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Pervaiz N, Shakeel N, Qasim A, Zehra R, Anwar S, Rana N, Xue Y, Zhang Z, Bao Y, Abbasi AA. Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evol Biol 2019; 19:128. [PMID: 31221090 PMCID: PMC6585022 DOI: 10.1186/s12862-019-1441-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. Three-way and Four-way paralogy regions in human and other vertebrate genomes are considered as vital evidence to support this hypothesis. Alternatively, it has been proposed that such paralogy regions are created by small-scale duplications that occurred at different intervals over the evolution of life. RESULTS To address this debate, the present study investigates the evolutionary history of multigene families with at least three-fold representation on human chromosomes 1, 2, 8 and 20. Phylogenetic analysis and the tree topology comparisons classified the members of 36 multigene families into four distinct co-duplicated groups. Gene families falling within the same co-duplicated group might have duplicated together, whereas genes belong to different co-duplicated groups might have distinct evolutionary origins. CONCLUSION Taken together with previous investigations, the current study yielded no proof in favor of WGDs hypothesis. Rather, it appears that the vertebrate genome evolved as a result of small-scale duplication events, that cover the entire span of the animals' history.
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Affiliation(s)
- Nashaiman Pervaiz
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nazia Shakeel
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ayesha Qasim
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rabail Zehra
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Saneela Anwar
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Neenish Rana
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yongbiao Xue
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Haq F, Saeed U, Khalid R, Qasim M, Mehmood M. Phylogenetic analyses of human 1/2/8/20 paralogons suggest segmental duplications during animal evolution. 3 Biotech 2019; 9:233. [PMID: 31139548 DOI: 10.1007/s13205-019-1768-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/16/2019] [Indexed: 11/28/2022] Open
Abstract
Susumu Ohno hypothesized that the diversity of vertebrate gene families and genome is due to two rounds of whole genome duplications (also referred as 2R hypothesis). The quadruplicate paralogous blocks present on 1/2/8/20 chromosomes are taken as one of the evidences in favor of the 2R. In this study, we investigated that whether 2R has shaped the vertebrate evolution using gene families residing on chromosomes 1/2/8/20. Evolutionary history of 22 gene families (11 from the current study and 11 from the previous study) was evaluated by the phylogenetic analysis with triplicated or quadruplicated distribution on these human chromosomes 1/2/8/20. The phylogenetic analysis was performed using high-quality whole genomic sequence data of multiple species with neighbor-joining (NJ) and maximum likelihood (ML) methods. The phylogenetic tree topology of these gene families revealed variable duplication time points during invertebrate-vertebrate evolution. Topology comparison approach categorized 22 gene families into three groups. Tree topologies of ten gene families fell into Group 1 (duplications prior to invertebrate-vertebrate split), four in Group 2 (i.e., (AB) (C) (D), topology incongruent with 2R) and eight in Group 3 (((AB) (CD)), 2R congruent topology). Therefore, taken together the current and previous data of 1/2/8/20 paralogons, we propose that, in addition to whole genome duplications events, current developmental, morphological and genomic complexity of the vertebrate genomes may also have originated through segmental duplications occurring at varying time points during the course of animal evolution.
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Affiliation(s)
- Farhan Haq
- 1Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shehzad, Islamabad, Pakistan
| | - Usman Saeed
- 2Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Munich, Germany
| | - Rida Khalid
- 1Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shehzad, Islamabad, Pakistan
| | | | - Maryam Mehmood
- 1Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shehzad, Islamabad, Pakistan
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Naz R, Tahir S, Abbasi AA. An insight into the evolutionary history of human MHC paralogon. Mol Phylogenet Evol 2017; 110:1-6. [PMID: 28249742 DOI: 10.1016/j.ympev.2017.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 02/20/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
The vertebrate genome contains several closely spaced sets of paralogous genes from distinct gene families on typically two, three or four different chromosomes (paralogons). These four fold paralogy regions have been considered as historical remnants of whole genome duplication events (WGDs/2R hypothesis). To examine the 2R hypothesis, a robust phylogenetic analysis of 40 multigene families with triplicated or quadruplicated distribution on human MHC bearing chromosomes (1/6/9/19) was conducted. Topology comparison approach categorized the members of 40 families into six distinct co-duplicated groups. Genes belonging to a particular co-duplicated group are duplicated concurrently, whereas genes of two different co-duplicated groups do not share their evolutionary history and have not duplicated in harmony. Our results based on this large scale phylogenetic data set contradict the polyploidization model and are indicative of small-scale duplications and rearrangement events that cover the entire span of animal history.
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Affiliation(s)
- Roheena Naz
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sadaf Tahir
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Abstract
Hox proteins are a deeply conserved group of transcription factors originally defined for their critical roles in governing segmental identity along the antero-posterior (AP) axis in
Drosophila. Over the last 30 years, numerous data generated in evolutionarily diverse taxa have clearly shown that changes in the expression patterns of these genes are closely associated with the regionalization of the AP axis, suggesting that
Hox genes have played a critical role in the evolution of novel body plans within Bilateria. Despite this deep functional conservation and the importance of these genes in AP patterning, key questions remain regarding many aspects of
Hox biology. In this commentary, we highlight recent reports that have provided novel insight into the origins of the mammalian
Hox cluster, the role of
Hox genes in the generation of a limbless body plan, and a novel putative mechanism in which
Hox genes may encode specificity along the AP axis. Although the data discussed here offer a fresh perspective, it is clear that there is still much to learn about
Hox biology and the roles it has played in the evolution of the Bilaterian body plan.
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Affiliation(s)
- Steven M Hrycaj
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA
| | - Deneen M Wellik
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA
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Abbasi AA. Diversification of four human HOX gene clusters by step-wise evolution rather than ancient whole-genome duplications. Dev Genes Evol 2015; 225:353-7. [PMID: 26481129 DOI: 10.1007/s00427-015-0518-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/08/2015] [Indexed: 12/30/2022]
Abstract
HOX genes encode transcriptional factors that play a pivotal role in specifying regional identity in nearly every bilateral animal. The birth of HOX gene cluster and its subsequent evolution, either in regulation or function, underlie the evolution of many bilaterian features and hence to the evolutionary radiation of this group. Despite of this importance, evolution of HOX cluster in vertebrates remains largely obscure because the phylogenetic history of these genes is poorly resolved. This has led to the controversy about whether four HOX clusters in human originated through two rounds (2R) of whole-genome duplications or instead evolved by small-scale events early in vertebrate evolution. Recently, the large-scale phylogenetic analysis of triplicate and quadruplicate paralogous regions residing on human HOX-bearing chromosomes provided an unprecedented insight into events that shaped vertebrate genome early in their history. Based on these data and comparative genomic analysis of fruit fly, red floor beetle, and human, this study infers the genic content of minimal HOX locus in the Urbilaterian and reconstructs its duplication history. It appears that four HOX clusters of humans are not remnants of polyploidy events in vertebrate ancestry. Rather, current evidence suggests that one-to-four transition in HOX cluster number occurred by three-step sequential process involving regional duplication events. Therefore, it is concluded that the evolutionary origin of vertebrate novelties, including the complexity of their body, is the consequence of small-scale genetic changes at widely different times over their history.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Hafeez M, Shabbir M, Altaf F, Abbasi AA. Phylogenomic analysis reveals ancient segmental duplications in the human genome. Mol Phylogenet Evol 2015; 94:95-100. [PMID: 26327327 DOI: 10.1016/j.ympev.2015.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/04/2015] [Accepted: 08/21/2015] [Indexed: 01/16/2023]
Abstract
Evolution of organismal complexity and origin of novelties during vertebrate history has been widely explored in context of both regulation of gene expression and gene duplication events. Ohno (1970) for the first time put forward the idea of two rounds whole genome duplication events as the most plausible explanation for evolutionarizing the vertebrate lineage (2R hypothesis). To test the validity of 2R hypothesis, a robust phylogenomic analysis of multigene families with triplicated or quadruplicated representation on human FGFR bearing chromosomes (4/5/8/10) was performed. Topology comparison approach categorized members of 80 families into five distinct co-duplicated groups. Genes belonging to one co-duplicated group are duplicated concurrently, whereas genes of two different co-duplicated groups do not share their duplication history and have not duplicated in congruency. Our findings contradict the 2R model and are indicative of small-scale duplications and rearrangements that cover the entire span of animal's history.
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Affiliation(s)
- Madiha Hafeez
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Madiha Shabbir
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Fouzia Altaf
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution. Mol Phylogenet Evol 2014; 81:49-60. [PMID: 25245952 DOI: 10.1016/j.ympev.2014.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 11/23/2022]
Abstract
BACKGROUND Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history. RESULTS Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently. CONCLUSION Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life.
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10
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Ambreen S, Khalil F, Abbasi AA. Integrating large-scale phylogenetic datasets to dissect the ancient evolutionary history of vertebrate genome. Mol Phylogenet Evol 2014; 78:1-13. [PMID: 24821622 DOI: 10.1016/j.ympev.2014.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/17/2014] [Accepted: 05/01/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND The vertebrate genome often contains closely spaced set of paralogous genes from distinct gene families on typically two, three or four different chromosomes (paralogons). This type of genome architecture is widely considered to be remnants of whole genome duplication events (WGD/2R). RESULTS Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the evolutionary history of potential quadruplicated regions residing on human HOX-cluster bearing chromosomes (chromosomes 2/7/12/17). For this purpose a detailed phylogenetic analysis was performed for those multigene families, including members of at least three of the four HOX-bearing chromosomes. Topology comparison approach categorized the members of 63 families into distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated concurrently, whereas genes of two different co-duplicated groups do not share their history and have not duplicated in concert with each other. CONCLUSIONS These results based on large-scale phylogenetic dataset yielded no evidence in favor of polyploidization events; instead it appears that triplicated and quadruplicated genomic segments on the human HOX-bearing chromosomes arose by small-scale duplication events that occurred at widely different time points in animal evolution.
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Affiliation(s)
- Sadaf Ambreen
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Faiqa Khalil
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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11
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Asrar Z, Haq F, Abbasi AA. Fourfold paralogy regions on human HOX-bearing chromosomes: role of ancient segmental duplications in the evolution of vertebrate genome. Mol Phylogenet Evol 2012; 66:737-47. [PMID: 23142696 DOI: 10.1016/j.ympev.2012.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 10/27/2012] [Accepted: 10/29/2012] [Indexed: 01/26/2023]
Abstract
BACKGROUND Susumu Ohno's idea that modern vertebrates are degenerate polyploids (concept referred as 2R hypothesis) has been the subject of intense debate for past four decades. It was proposed that intra-genomic synteny regions (paralogons) in human genome are remains of ancient polyploidization events that occurred early in the vertebrate history. The quadruplicated paralogon centered on human HOX clusters is taken as evidence that human HOX-bearing chromosomes were structured by two rounds of whole genome duplication (WGD) events. RESULTS Evolutionary history of human HOX-bearing chromosomes (chromosomes 2/7/12/17) was evaluated by the phylogenetic analysis of multigene families with triplicated or quadruplicated distribution on these chromosomes. Topology comparison approach categorized the members of 44 families into four distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated simultaneously, whereas genes of two distinct co-duplicated groups do not share their evolutionary history and have not duplicated in concert with each other. CONCLUSION The recovery of co-duplicated groups suggests that "ancient segmental duplications and rearrangements" is the most rational model of evolutionary events that have generated the triplicated and quadruplicated paralogy regions seen on the human HOX-bearing chromosomes.
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Affiliation(s)
- Zainab Asrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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12
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Abbasi AA, Hanif H. Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20 provides no evidence in favor of the vertebrate octoploidy hypothesis. Mol Phylogenet Evol 2012; 63:922-7. [PMID: 22425707 DOI: 10.1016/j.ympev.2012.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 02/08/2012] [Accepted: 02/27/2012] [Indexed: 01/24/2023]
Abstract
Fourfold paralogy regions in the human genome have been considered historical remnants of whole-genome duplication events predicted to have occurred early in vertebrate evolution. Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the prediction that the ancestral vertebrate genome was shaped by two rapid rounds of whole-genome duplication within a period of 10 million years. Both the map self-comparison approach and a phylogenetic analysis revealed that gene families identified as tetralogous on human chromosomes 1/2/8/20 arose by small-scale duplication events that occurred at widely different time points in animal evolution. Furthermore, the data discount the likelihood that tree topologies of the form ((A,B)(C,D)) are best explained by the octoploidy hypothesis. We instead propose that such symmetrical tree patterns are also consistent with local duplications and rearrangement events.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Nomiyama H, Osada N, Yoshie O. A family tree of vertebrate chemokine receptors for a unified nomenclature. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:705-715. [PMID: 21295066 DOI: 10.1016/j.dci.2011.01.019] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 05/30/2023]
Abstract
Chemokines receptors are involved in the recruitment of various cell types in inflammatory and physiological conditions. There are 23 known chemokine receptor genes in the human genome. However, it is still unclear how many chemokine receptors exist in the genomes of various vertebrate species other than human and mouse. Moreover, the orthologous relationships are often obscure between the genes of higher and lower vertebrates. In order to provide a basis for a unified nomenclature system of the vertebrate chemokine receptor gene family, we have analysed the chemokine receptor genes from the genomes of 16 vertebrate species, and classify them into 29 orthologous groups using phylogenetic and comparative genomic analyses. The results reveal a continuous gene birth and death process during the vertebrate evolution and an interesting evolutionary history of the chemokine receptor genes after the emergence in agnathans.
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Affiliation(s)
- Hisayuki Nomiyama
- Department of Molecular Enzymology, Kumamoto University Faculty of Life Sciences, Honjo, Kumamoto 860-8556, Japan.
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Daza DO, Sundström G, Bergqvist CA, Duan C, Larhammar D. Evolution of the insulin-like growth factor binding protein (IGFBP) family. Endocrinology 2011; 152:2278-89. [PMID: 21505050 DOI: 10.1210/en.2011-0047] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both chromosomal and serial duplications have been suggested as mechanisms for the expansion of this gene family. We have identified and annotated IGFBP sequences from a wide selection of vertebrate species as well as Branchiostoma floridae and Ciona intestinalis. By combining detailed sequence analysis with sequence-based phylogenies and chromosome information, we arrive at the following scenario: the ancestral chordate IGFBP gene underwent a local gene duplication, resulting in a gene pair adjacent to a HOX cluster. Subsequently, the gene family expanded in the two basal vertebrate tetraploidization (2R) resulting in the six IGFBP types that are presently found in placental mammals. The teleost fish ancestor underwent a third tetraploidization (3R) that further expanded the IGFBP repertoire. The five sequenced teleost fish genomes retain 9-11 of IGFBP genes. This scenario is supported by the phylogenies of three adjacent gene families in the HOX gene regions, namely the epidermal growth factor receptors (EGFR) and the Ikaros and distal-less (DLX) transcription factors. Our sequence comparisons show that several important structural components in the IGFBPs are ancestral vertebrate features that have been maintained in all orthologs, for instance the integrin interaction motif Arg-Gly-Asp in IGFBP-2. In contrast, the Arg-Gly-Asp motif in IGFBP-1 has arisen independently in mammals. The large degree of retention of IGFBP genes after the ancient expansion of the gene family strongly suggests that each gene evolved distinct and important functions early in vertebrate evolution.
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Shimizu M, Suzuki S, Horikoshi M, Hara A, Dickhoff WW. Circulating salmon 41-kDa insulin-like growth factor binding protein (IGFBP) is not IGFBP-3 but an IGFBP-2 subtype. Gen Comp Endocrinol 2011; 171:326-31. [PMID: 21354155 DOI: 10.1016/j.ygcen.2011.02.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 01/23/2011] [Accepted: 02/20/2011] [Indexed: 11/17/2022]
Abstract
In vertebrates, most circulating insulin-like growth factor (IGF) is bound to multiple forms of IGF-binding proteins (IGFBPs) that differ both structurally and functionally. In mammals, the largest reservoir of IGF in the circulation comes from a large (150kDa) ternary complex comprised of IGF bound to IGFBP-3, which is bound to an acid label subunit (ALS), and this variant of IGFBP is regulated by growth hormone (GH) and feed intake. Although multiple variants of IGFBPs ranging from 20 to 50kDa have been found in fishes, no ternary complex is present and it has been assumed that the majority of circulating IGF is bound to fish IGFBP-3. Consistent with this assumption is previous work in salmon showing the presence of a 41-kDa IGFBP that is stimulated by GH, decreases with fasting and increases with feeding. However, the hypothesis that the salmon 41-kDa IGFBP is structurally homologous to mammalian IGFBP-3 has not been directly tested. To address this issue, we cloned cDNAs for several Chinook salmon IGFBPs, and found that the cDNA sequence of the 41-kDa IGFBP is most similar to that of mammalian IGFBP-2 and dissimilar to IGFBP-3. We found an additional IGFBP (termed IGFBP-2a) with high homology to mammalian IGFBP-2. These results demonstrate that salmon 41-kDa IGFBP is not IGFBP-3, but a paralog of IGFBP-2 (termed IGFBP-2b). Salmon IGFBP-2s are also unique in terms of having potential N-glycosylation sites and splice variants. Additional research on non-mammalian IGFBPs is needed to fully understand the molecular/functional evolution of the IGFBP family and the significance of the ternary complex in vertebrates.
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Affiliation(s)
- Munetaka Shimizu
- Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido 041-8611, Japan.
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Abbasi AA. Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX-cluster paralogons. Mol Phylogenet Evol 2010; 57:836-48. [PMID: 20696259 DOI: 10.1016/j.ympev.2010.07.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 07/21/2010] [Accepted: 07/27/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND Vertebrate genomes contain extensive intra-genomic conserved synteny, which is the presence of similar set of genes on two or more chromosomes (paralogons). The existence of these paralogons has led to the proposal that vertebrate genome was structured by one or more rounds of ancient whole genome duplications (2R hypothesis). RESULTS The 2R hypothesis was tested by phylogenetic analysis of gene families residing on human HOX-bearing chromosomes (HOX-cluster paralogons). These results revealed that, based on their duplication history, 23 gene families with representation on three or four of the human HOX-bearing chromosomes can be partitioned into four discrete co-duplicated groups. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups do not share their evolutionary history and are not duplicated simultaneously. These co-duplicated groups are large constituting members from 3 to 8 gene families and suggest that human HOX-cluster paralogons were shaped by ancient segmental duplications (SDs) and rearrangement events that occurred at least as early as before the divergence of bony fishes and tetrapods. CONCLUSIONS Based on the recovery of ancient SD events in this analysis and given the widespread evidence in favor of the fact that recent SD events played a pivotal role in changing genome architecture of primates and other recently diverged animals, it is concluded that a more realistic model of ancient vertebrate genome evolutionary history can be deduced by tracing the evolutionary trajectory of the genomes of recently diverged vertebrate species.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. BMC DEVELOPMENTAL BIOLOGY 2010; 10:44. [PMID: 20426846 PMCID: PMC2875213 DOI: 10.1186/1471-213x-10-44] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 04/28/2010] [Indexed: 11/18/2022]
Abstract
Background The zinc-finger transcription factor GLI3 is an important mediator of Sonic hedgehog signaling and crucial for patterning of many aspects of the vertebrate body plan. In vertebrates, the mechanism of SHH signal transduction and its action on target genes by means of activating or repressing forms of GLI3 have been studied most extensively during limb development and the specification of the central nervous system. From these studies it has emerged, that Gli3 expression must be subject to a tight spatiotemporal regulation. However, the genetic mechanisms and the cis-acting elements controlling the expression of Gli3 remained largely unknown. Results Here, we demonstrate in chicken and mouse transgenic embryos that human GLI3-intronic conserved non-coding sequence elements (CNEs) autonomously control individual aspects of Gli3 expression. Their combined action shows many aspects of a Gli3-specific pattern of transcriptional activity. In the mouse limb bud, different CNEs enhance Gli3-specific expression in evolutionary ancient stylopod and zeugopod versus modern skeletal structures of the autopod. Limb bud specificity is also found in chicken but had not been detected in zebrafish embryos. Three of these elements govern central nervous system specific gene expression during mouse embryogenesis, each targeting a subset of endogenous Gli3 transcription sites. Even though fish, birds, and mammals share an ancient repertoire of gene regulatory elements within Gli3, the functions of individual enhancers from this catalog have diverged significantly. During evolution, ancient broad-range regulatory elements within Gli3 attained higher specificity, critical for patterning of more specialized structures, by abolishing the potential for redundant expression control. Conclusion These results not only demonstrate the high level of complexity in the genetic mechanisms controlling Gli3 expression, but also reveal the evolutionary significance of cis-acting regulatory networks of early developmental regulators in vertebrates.
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Schaeper ND, Prpic NM, Wimmer EA. A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location. BMC Evol Biol 2010; 10:88. [PMID: 20353601 PMCID: PMC3087555 DOI: 10.1186/1471-2148-10-88] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 03/30/2010] [Indexed: 12/28/2022] Open
Abstract
Background The Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially discussed. This is especially the case for the Sp gene buttonhead (btd) which plays a key role in head development in Drosophila melanogaster, and has been proposed to have originated by a recent gene duplication. The purpose of the presented study was to trace orthologs of btd in other insects and reconstruct the evolutionary history of the Sp genes within the metazoa. Results We isolated Sp genes from representatives of a holometabolous insect (Tribolium castaneum), a hemimetabolous insect (Oncopeltus fasciatus), primitively wingless hexapods (Folsomia candida and Thermobia domestica), and an amphipod crustacean (Parhyale hawaienis). We supplemented this data set with data from fully sequenced animal genomes. We performed phylogenetic sequence analysis with the result that all Sp factors fall into three monophyletic clades. These clades are also supported by protein domain structure, gene expression, and chromosomal location. We show that clear orthologs of the D. melanogaster btd gene are present even in the basal insects, and that the Sp5-related genes in the genome sequence of several deuterostomes and the basal metazoans Trichoplax adhaerens and Nematostella vectensis are also orthologs of btd. Conclusions All available data provide strong evidence for an ancestral cluster of three Sp-family genes as well as synteny of this Sp cluster and the Hox cluster. The ancestral Sp gene cluster already contained a Sp5/btd ortholog, which strongly suggests that btd is not the result of a recent gene duplication, but directly traces back to an ancestral gene already present in the metazoan ancestor.
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Affiliation(s)
- Nina D Schaeper
- Georg-August-Universität, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung Entwicklungsbiologie, GZMB, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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Zhu J, Braun EL, Kohno S, Antenos M, Xu EY, Cook RW, Lin SJ, Moore BC, Guillette LJ, Jardetzky TS, Woodruff TK. Phylogenomic analyses reveal the evolutionary origin of the inhibin alpha-subunit, a unique TGFbeta superfamily antagonist. PLoS One 2010; 5:e9457. [PMID: 20209104 PMCID: PMC2832003 DOI: 10.1371/journal.pone.0009457] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 02/01/2010] [Indexed: 11/18/2022] Open
Abstract
Transforming growth factor-beta (TGFβ) homologues form a diverse superfamily that arose early in animal evolution and control cellular function through membrane-spanning, conserved serine-threonine kinases (RII and RI receptors). Activin and inhibin are related dimers within the TGFβ superfamily that share a common β-subunit. The evolution of the inhibin α-subunit created the only antagonist within the TGFβ superfamily and the only member known to act as an endocrine hormone. This hormone introduced a new level of complexity and control to vertebrate reproductive function. The novel functions of the inhibin α-subunit appear to reflect specific insertion-deletion changes within the inhibin β-subunit that occurred during evolution. Using phylogenomic analysis, we correlated specific insertions with the acquisition of distinct functions that underlie the phenotypic complexity of vertebrate reproductive processes. This phylogenomic approach presents a new way of understanding the structure-function relationships between inhibin, activin, and the larger TGFβ superfamily.
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Affiliation(s)
- Jie Zhu
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Satomi Kohno
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Monica Antenos
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Eugene Y. Xu
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Robert W. Cook
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - S. Jack Lin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Brandon C. Moore
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Louis J. Guillette
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Teresa K. Woodruff
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
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Abbasi AA. Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events. Nat Rev Genet 2010; 11:166. [PMID: 20051988 DOI: 10.1038/nrg2600-c1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abbasi AA, Goode DK, Amir S, Grzeschik KH. Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evol Bioinform Online 2009; 5:5-13. [PMID: 19812723 PMCID: PMC2747127 DOI: 10.4137/ebo.s2322] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background In vertebrates the “SONIC HEDGEHOG” signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1, GLI2 and GLI3) are key mediators of hedgehog morphogenetic signals, over the past couple of decades they have been extensively scrutinized by genetic, molecular and biochemical means. Thus, a great deal of information is currently available about the functional aspects of GLI proteins in various vertebrate species. To address the roles of GLI genes in diversifying the repertoire of the Hh signalling and deploying them for the vertebrate specifications, in this study we have examined the evolutionary patterns of vertebrate GLI sequences within and between species. Results Phylogenetic tree analysis suggests that the vertebrate GLI1, GLI2 and GLI3 genes diverged after the separation of urochordates from vertebrates and before the tetrapods-bony fishes split. Lineage specific duplication events were also detected. Estimation of mode and strength of selection acting on GLI orthologs demonstrated that all members of the GLI gene family experienced more relaxed selection in teleost fish than in the mammalian lineage. Furthermore, the GLI1 gene appeared to have been exposed to different functional constraints in fish and tetrapod lineages, whilst a similar level of functional constraints on GLI2 and GLI3 was suggested by comparable average non-synonymous (Ka) substitutions across the lineages. A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolved with similar evolutionary rates except GLI1 which evolved at a significantly faster rate than its paralogous counterparts in tetrapods. Conclusions Our analysis shows that sequence evolutionary patterns of GLI family members are largely correlated with the reported similarities and differences in the functionality of GLI proteins within and between the various vertebrate species. We propose that duplication and divergence of GLI genes has increased in the complexity of vertebrate body plan by recruiting the hedgehog signalling for the novel developmental tasks.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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22
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A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009; 10:252-63. [PMID: 19274049 DOI: 10.1038/nrg2538] [Citation(s) in RCA: 1095] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many transcription factors does the human genome contain? How are they expressed in different tissues? Are they evolutionarily conserved? Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation. Much remains to be explored, but this study provides a solid foundation for future investigations to elucidate regulatory mechanisms underlying diverse mammalian biological processes.
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Braasch I, Volff JN, Schartl M. The endothelin system: evolution of vertebrate-specific ligand-receptor interactions by three rounds of genome duplication. Mol Biol Evol 2009; 26:783-99. [PMID: 19174480 DOI: 10.1093/molbev/msp015] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Morphological innovations like the acquisition of the neural crest as well as gene family expansions by genome duplication are considered as major leaps in the evolution of the vertebrate lineage. Using comparative genomic analyses, we have reconstructed the evolutionary history of the endothelin system, a signaling pathway consisting of endothelin ligands and their G protein-coupled receptors. The endothelin system plays a key role in cardiovascular regulation as well as in the development of diverse neural crest derivatives like pigment cells and craniofacial bone structures, which are hot spots of diversity in vertebrates. However, little is known about the origin and evolution of the endothelin system in the vertebrate lineage. We show that the endothelin core system, that is, endothelin ligands (Edn) and their receptors (Ednr), is a vertebrate-specific innovation. The components of the endothelin core system in modern vertebrate genomes date back to single genes that have been duplicated during whole-genome duplication events. After two rounds of genome duplication during early vertebrate evolution, the endothelin system of an ancestral gnathostome consisted of four ligand and four receptor genes. The previously unknown fourth endothelin ligand Edn4 has been kept in teleost fish but lost in tetrapods. Bony vertebrates generally possess three receptor genes, EdnrA, EdnrB1, and EdnrB2. EdnrB2 has been lost secondarily in the mammalian lineage from a chromosome that gave rise to the sex chromosomes in therians (marsupials and placentals). The endothelin system of fishes was further expanded by a fish-specific genome duplication and duplicated edn2, edn3, ednrA, and ednrB1 genes have been retained in teleost fishes. Functional divergence analyses suppose that following each round of genome duplication, coevolution of ligands and their binding regions in the receptors has occurred, adjusting the endothelin signaling system to the increase of possible ligand-receptor interactions. Furthermore, duplications of genes involved in the endothelin system are associated with functional specialization for the development of particular neural crest derivatives. Our results support an important role for newly emerging ligands and receptors as components of signaling pathways and their expansion through genome duplications in the evolution of the vertebrate neural crest.
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Affiliation(s)
- Ingo Braasch
- University of Würzburg, Biozentrum, Physiological Chemistry I, Germany.
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Abbasi AA. Are we degenerate tetraploids? More genomes, new facts. Biol Direct 2008; 3:50. [PMID: 19077184 PMCID: PMC2615429 DOI: 10.1186/1745-6150-3-50] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 12/10/2008] [Indexed: 02/03/2023] Open
Abstract
Background Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been associated with two genome duplications (2R hypothesis) at the origin of vertebrates. However, in spite of extensive debate the validity of the 2R hypothesis remains controversial. The paucity of sequence data in early years of genomic era was an intrinsic obstacle in tracking the genome evolutionary history of chordates. Hypothesis In this article I review the 2R hypothesis by taking into account the recent availability of genomic sequence data for an expanding range of animals. I argue here that genetic architecture of lower metazoans and representatives of major vertebrate and invertebrate lineages provides no support for the hypothesis relating the origin of vertebrates with widespread gene or genome duplications. Conclusion It appears that much of the genomic complexity of modern vertebrates is very ancient likely predating the origin of chordates or even the Bilaterian-Nonbilaterian divergence. The origin and evolution of vertebrates is partly accompanied by an increase in gene number. However, neither can we take this subtle increase in gene number as an only causative factor for evolution of phenotypic complexity in modern vertebrates nor we can take it as a reflection of polyplodization events early in their history. Reviewers This article was reviewed by Eugene Koonin, Joshua Cherry (nominated by David Lipman), and Jerzy Jurka.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
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Sundström G, Larsson TA, Larhammar D. Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters. BMC Evol Biol 2008; 8:254. [PMID: 18803835 PMCID: PMC2566581 DOI: 10.1186/1471-2148-8-254] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 09/19/2008] [Indexed: 12/15/2022] Open
Abstract
Background Ever since the theory about two rounds of genome duplication (2R) in the
vertebrate lineage was proposed, the Hox gene clusters have served as the
prime example of quadruplicate paralogy in mammalian genomes. In teleost
fishes, the observation of additional Hox clusters absent in other
vertebrate lineages suggested a third tetraploidization (3R). Because the
Hox clusters occupy a quite limited part of each chromosome, and are special
in having position-dependent regulation within the multi-gene cluster,
studies of syntenic gene families are needed to determine the extent of the
duplicated chromosome segments. We have analyzed in detail 14 gene families
that are syntenic with the Hox clusters to see if their phylogenies are
compatible with the Hox duplications and the 2R/3R scenario. Our starting
point was the gene family for the NPY family of peptides located near the
Hox clusters in the pufferfish Takifugu rubripes, the zebrafish
Danio rerio, and human. Results Seven of the gene families have members on at least three of the human Hox
chromosomes and two families are present on all four. Using both
neighbor-joining and quartet-puzzling maximum likelihood methods we found
that 13 families have a phylogeny that supports duplications coinciding with
the Hox cluster duplications. One additional family also has a topology
consistent with 2R but due to lack of urochordate or cephalocordate
sequences the time window when these duplications could have occurred is
wider. All but two gene families also show teleost-specific duplicates. Conclusion Based on this analysis we conclude that the Hox cluster duplications involved
a large number of adjacent gene families, supporting expansion of these
families in the 2R, as well as in the teleost 3R tetraploidization. The gene
duplicates presumably provided raw material in early vertebrate evolution
for neofunctionalization and subfunctionalization.
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Affiliation(s)
- Görel Sundström
- Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden.
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Genome duplication and the origin of the vertebrate skeleton. Curr Opin Genet Dev 2008; 18:387-93. [PMID: 18721879 DOI: 10.1016/j.gde.2008.07.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 06/26/2008] [Accepted: 07/21/2008] [Indexed: 11/22/2022]
Abstract
During vertebrate embryonic development, tissue patterning and differentiation are regulated by members of multigene families. Evolutionary expansion of these families is thought to have played a role in the evolution of anatomical complexity, including the origins of new cell and tissue types. A defining feature of vertebrates is an endoskeleton, the primary components of which are cartilage and bone. The molecular control of skeletal patterning has been the subject of intensive investigation for over two decades. More recently, comparative studies of organisms at key phylogenetic positions have highlighted the importance of gene duplication in the evolutionary diversification of connective tissues. Understanding the natural histories of gene families involved in skeletogenesis is therefore central to the issue of vertebrate skeletal evolution.
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Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D. Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions. BMC Evol Biol 2008; 8:184. [PMID: 18578868 PMCID: PMC2453138 DOI: 10.1186/1471-2148-8-184] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 06/25/2008] [Indexed: 12/31/2022] Open
Abstract
Background One of the many gene families that expanded in early vertebrate evolution is the neuropeptide (NPY) receptor family of G-protein coupled receptors. Earlier work by our lab suggested that several of the NPY receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes) and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. In this study we have investigated, in five vertebrate genomes, 45 gene families with members close to the NPY receptor genes in the compact genomes of the teleost fishes Tetraodon nigroviridis and Takifugu rubripes. These correspond to Homo sapiens chromosomes 4, 5, 8 and 10. Results Chromosome regions with conserved synteny were identified and confirmed by phylogenetic analyses in H. sapiens, M. musculus, D. rerio, T. rubripes and T. nigroviridis. 26 gene families, including the NPY receptor genes, (plus 3 described recently by other labs) showed a tree topology consistent with duplications in early vertebrate evolution and in the actinopterygian lineage, thereby supporting expansion through block duplications. Eight gene families had complications that precluded analysis (such as short sequence length or variable number of repeated domains) and another eight families did not support block duplications (because the paralogs in these families seem to have originated in another time window than the proposed genome duplication events). RT-PCR carried out with several tissues in T. rubripes revealed that all five NPY receptors were expressed in the brain and subtypes Y2, Y4 and Y8 were also expressed in peripheral organs. Conclusion We conclude that the phylogenetic analyses and chromosomal locations of these gene families support duplications of large blocks of genes or even entire chromosomes. Thus, these results are consistent with two early vertebrate tetraploidizations forming a paralogon comprising human chromosomes 4, 5, 8 and 10 and one teleost tetraploidization. The combination of positional and phylogenetic data further strengthens the identification of orthologs and paralogs in the NPY receptor family.
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Affiliation(s)
- Tomas A Larsson
- Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden.
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Kim S, Jung G, Lee J, Park H, Kim C. A phylogenetic analysis for K‐Hox linked gene families of vertebrates. Anim Cells Syst (Seoul) 2008. [DOI: 10.1080/19768354.2008.9647181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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