1
|
Kosuthova K, Solc R. Inversions on human chromosomes. Am J Med Genet A 2023; 191:672-683. [PMID: 36495134 DOI: 10.1002/ajmg.a.63063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Human chromosome inversions are types of balanced structural variations, making them difficult to analyze. Thanks to PEM (paired-end sequencing and mapping), there has been tremendous progress in studying inversions. Inversions play an important role as an evolutionary factor, contributing to the formation of gonosomes, speciation of chimpanzees and humans, and inv17q21.3 or inv8p23.1 exhibit the features of natural selection. Both inversions have been related to pathogenic phenotype by directly affecting a gene structure (e.g., inv5p15.1q14.1), regulating gene expression (e.g., inv7q21.3q35) and by predisposing to other secondary arrangements (e.g., inv7q11.23). A polymorphism of human inversions is documented by the InvFEST database (a database that stores information about clinical predictions, validations, frequency of inversions, etc.), but only a small fraction of these inversions is validated, and a detailed analysis is complicated by the frequent location of breakpoints within regions of repetitive sequences.
Collapse
Affiliation(s)
- Klara Kosuthova
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
2
|
Waters PD, Patel HR, Ruiz-Herrera A, Álvarez-González L, Lister NC, Simakov O, Ezaz T, Kaur P, Frere C, Grützner F, Georges A, Graves JAM. Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proc Natl Acad Sci U S A 2021; 118:e2112494118. [PMID: 34725164 PMCID: PMC8609325 DOI: 10.1073/pnas.2112494118] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Microchromosomes, once considered unimportant shreds of the chicken genome, are gene-rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole-genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds, and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly, de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early-branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently, multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus, microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles and birds, that are atypical.
Collapse
Affiliation(s)
- Paul D Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Hardip R Patel
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, 1010 Vienna, Austria
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
| | - Celine Frere
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3068, Australia
| |
Collapse
|
3
|
Ferreira M, de Jesus IS, Viana PF, Garcia C, Matoso DA, Cioffi MB, Bertollo LAC, Feldberg E. Chromosomal Evolution in Aspredinidae (Teleostei, Siluriformes): Insights on Intra- and Interspecific Relationships with Related Groups. Cytogenet Genome Res 2020; 160:539-553. [PMID: 33227787 DOI: 10.1159/000511125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/22/2020] [Indexed: 11/19/2022] Open
Abstract
The family Aspredinidae comprises a clade of complex systematic relationships, both from molecular and morphological approaches. In this study, conventional and molecular cytogenetic studies coupled with nucleotide sequencing were performed in 6 Aspredininae species (Amaralia hypsiura, Bunocephalus cf. aloikae, Bunocephalus amaurus, Bunocephalus aff. coracoideus, Bunocephalus verrucosus, and Platystacus cotylephorus) from different locations of the Amazon hydrographic basin. Our results showed highly divergent diploid numbers (2n) among the species, ranging from 49 to 74, including the occurrence of an XX/X0 sex chromosome system. A neighbor-joining phylogram based on the cytochrome c oxidase I (COI) showed that Bunocephalus coracoideus is not a monophyletic clade, but closely related to B. verrucosus. The karyotypic data associated with COI suggest an ancestral karyotype for Aspredinidae with a reduced 2n, composed of bi-armed chromosomes and a trend toward chromosomal fissions resulting in higher diploid number karyotypes, mainly composed of acrocentric chromosomes. Evolutionary relationships were discussed under a phylogenetic context with related species from different Siluriformes families. The karyotype features and chromosomal diversity of Aspredinidae show an amazing differentiation, making this family a remarkable model for investigating the evolutionary dynamics in siluriforms as well as in fish as a whole.
Collapse
Affiliation(s)
- Milena Ferreira
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Secretaria de Estado de Educação e Qualidade do Ensino (SEDUC), Manaus, Brazil
| | - Isac S de Jesus
- Laboratório de Fisiologia Comportamental e Evolução, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik F Viana
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Caroline Garcia
- Laboratório de Citogenética, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Daniele A Matoso
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil,
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| |
Collapse
|
4
|
Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
Collapse
Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| |
Collapse
|
5
|
Walker LI, Soto MA, Spotorno ÁE. Similarities and differences among the chromosomes of the wild guinea pig Cavia tschudii and the domestic guinea pig Cavia porcellus (Rodentia, Caviidae). COMPARATIVE CYTOGENETICS 2014; 8:153-67. [PMID: 25147626 PMCID: PMC4137285 DOI: 10.3897/compcytogen.v8i2.7509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/10/2014] [Indexed: 06/02/2023]
Abstract
Cavia tschudii Fitzinger, 1867 is a wild guinea pig species living in South America that according to the analysis of mitochondrial genes is the closest wild form of the domestic guinea pig. To investigate the genetic divergence between the wild and domestic species of guinea pigs from a cytogenetic perspective, we characterized and compared the C, G and AgNOR banded karyotypes of molecularly identified Cavia tschudii and Cavia porcellus Linnaeus, 1758 specimens for the first time. Both species showed 64 chromosomes of similar morphology, although C. tschudii had four medium size submetacentric pairs that were not observed in the C. porcellus karyotype. Differences in the C bands size and the mean number of AgNOR bands between the karyotypes of the two species were detected. Most of the two species chromosomes showed total G band correspondence, suggesting that they probably represent large syntenic blocks conserved over time. Partial G band correspondence detected among the four submetacentric chromosomes present only in the C. tschudii karyotype and their subtelocentric homologues in C. porcellus may be explained by the occurrence of four pericentric inversions that probably emerged and were fixed in the C. tschudii populations under domestication. The role of the chromosomal and genomic differences in the divergence of these two Cavia species is discussed.
Collapse
Affiliation(s)
- Laura I. Walker
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
| | - Miguel A. Soto
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
| | - Ángel E. Spotorno
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
| |
Collapse
|
6
|
Farré M, Micheletti D, Ruiz-Herrera A. Recombination rates and genomic shuffling in human and chimpanzee--a new twist in the chromosomal speciation theory. Mol Biol Evol 2012. [PMID: 23204393 PMCID: PMC3603309 DOI: 10.1093/molbev/mss272] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human-chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human-chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals.
Collapse
Affiliation(s)
- Marta Farré
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | | | | |
Collapse
|
7
|
An exon-based comparative variant analysis pipeline to study the scale and role of frameshift and nonsense mutation in the human-chimpanzee divergence. Comp Funct Genomics 2009:406421. [PMID: 19859573 PMCID: PMC2765723 DOI: 10.1155/2009/406421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 07/14/2009] [Accepted: 07/18/2009] [Indexed: 11/18/2022] Open
Abstract
Chimpanzees and humans are closely related but differ in many deadly human diseases and other characteristics in physiology, anatomy, and pathology. In spite of decades of extensive research, crucial questions about the
molecular mechanisms behind the differences are yet to be understood. Here I report ExonVar, a novel computational pipeline for Exon-based human-chimpanzee comparative Variant analysis. The objective is to comparatively
analyze mutations specifically those that caused the frameshift and nonsense mutations and to assess their scale and potential impacts on human-chimpanzee divergence. Genomewide analysis of human and chimpanzee exons with ExonVar identified a number of species-specific, exon-disrupting mutations in chimpanzees but much fewer in humans. Many were found on genes involved in
important biological processes such as T cell lineage development, the pathogenesis of inflammatory diseases, and antigen induced cell death. A “less-is-more” model was previously established to illustrate the role of the gene inactivation and disruptions during human evolution. Here this analysis suggested a different model where the chimpanzee-specific exon-disrupting mutations may act as additional evolutionary force that drove the human-chimpanzee divergence. Finally, the analysis revealed a number of sequencing errors in the chimpanzee and human genome sequences and further illustrated that they could be corrected without resequencing.
Collapse
|
8
|
Hannan FM, Nesbit MA, Turner JJO, Stacey JM, Cianferotti L, Christie PT, Conigrave AD, Whyte MP, Thakker RV. Comparison of human chromosome 19q13 and syntenic region on mouse chromosome 7 reveals absence, in man, of 11.6 Mb containing four mouse calcium-sensing receptor-related sequences: relevance to familial benign hypocalciuric hypercalcaemia type 3. Eur J Hum Genet 2009; 18:442-7. [PMID: 19809483 DOI: 10.1038/ejhg.2009.161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Familial benign hypocalciuric hypercalcaemia (FBHH) is a genetically heterogeneous disorder that consists of three designated types, FBHH1, FBHH2 and FBHH3, whose chromosomal locations are 3q21.1, 19p and 19q13, respectively. FBHH1 is caused by mutations of a calcium-sensing receptor (CaSR), but the abnormalities underlying FBHH2 and FBHH3 are unknown. FBHH3, also referred to as the Oklahoma variant (FBHH(Ok)), has been mapped to a 12cM interval, flanked by D19S908 and D19S866. To refine the location of FBHH3, we pursued linkage studies using 24 polymorphic loci. Our results establish a linkage between FBHH3 and 17 of these loci, and indicate that FBHH3 is located in a 4.1 Mb region flanked centromerically by D19S112 and telomerically by rs245111, which in the syntenic region on mouse chromosome 7 contains four Casr-related sequences (Gprc2a-rss). However, human homologues of these Gprc2a-rss were not found and a comparative analysis of the 22.0 Mb human and 39.3 Mb mouse syntenic regions showed evolutionary conservation of two segments that were inverted with loss from the human genome of 11.6 Mb that contained the four Gprc2a-rss. Thus, FBHH3 cannot be attributed to Gprc2a-rss abnormalities. DNA sequence analysis of 12 other genes from the interval that were expressed in the parathyroids and/or kidneys did not detect any abnormalities, thereby indicating that these genes are unlikely to be the cause of FBHH3. The results of this study have refined the map location of FBHH3, which will facilitate the identification of another CaSR or a mediator of calcium homeostasis.
Collapse
Affiliation(s)
- Fadil M Hannan
- Academic Endocrine Unit, Nuffield Department of Clinical Medicine, Churchill Hospital, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Lynch VJ, Wagner GP. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes. PLoS Genet 2009; 5:e1000349. [PMID: 19165336 PMCID: PMC2622764 DOI: 10.1371/journal.pgen.1000349] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 12/18/2008] [Indexed: 11/19/2022] Open
Abstract
While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion--such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these--is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model) occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox "paralogon") and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.
Collapse
Affiliation(s)
- Vincent J Lynch
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.
| | | |
Collapse
|
10
|
Symmons O, Váradi A, Arányi T. How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes. Mol Biol Evol 2008; 25:2601-13. [PMID: 18791038 DOI: 10.1093/molbev/msn202] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The completion of the Human Genome Project has brought the understanding that our genome contains an unexpectedly large proportion of segmental duplications. This poses the challenge of elucidating the consequences of recent duplications on physiology. We have conducted an in-depth study of a subset of segmental duplications on chromosome 16. We focused on PKD1 and ABCC6 duplications because mutations affecting these genes are responsible for the Mendelian disorders autosomal dominant polycystic kidney disease and pseudoxanthoma elasticum, respectively. We establish that duplications of PKD1 and ABCC6 are associated to low-copy repeat 16a and show that such duplications have occurred several times independently in different primate species. We demonstrate that partial duplication of PKD1 and ABCC6 has numerous consequences: the pseudogenes give rise to new transcripts and mediate gene conversion, which not only results in disease-causing mutations but also serves as a reservoir for sequence variation. The duplicated segments are also involved in submicroscopic and microscopic genomic rearrangements, contributing to structural variation in human and chromosomal break points in the gibbon. In conclusion, our data shed light on the recent and ongoing evolution of chromosome 16 mediated by segmental duplication and deepen our understanding of the history of two Mendelian disorder genes.
Collapse
Affiliation(s)
- Orsolya Symmons
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | | | | |
Collapse
|
11
|
Marques-Bonet T, Cheng Z, She X, Eichler EE, Navarro A. The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements. BMC Genomics 2008; 9:384. [PMID: 18699995 PMCID: PMC2542386 DOI: 10.1186/1471-2164-9-384] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 08/12/2008] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements. RESULTS Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. CONCLUSION We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.
Collapse
Affiliation(s)
- Tomàs Marques-Bonet
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Ze Cheng
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Xinwei She
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Arcadi Navarro
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA) and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Population Genomics Node (GNV8), National Institute for Bioinformatics (INB) Universitat Pompeu Fabra, Spain
| |
Collapse
|
12
|
Abstract
Reptiles are a karyologically heterogeneous group, where some orders and suborders exhibit characteristics similar to those of anamniotes and others share similarities with homeotherms. The class also shows different evolutionary trends, for instance in genome and chromosome size and composition. The turtle DNA base composition is similar to that of mammals, whereas that of lizards and snakes is more similar to that of anamniotes. The major karyological differences between turtles and squamates are the size and composition of the genome and the rate at which chromosomes change. Turtles have larger and more variable genome sizes, and a greater amount of middle repetitive DNA that differs even among related species. In lizards and snakes size of the genome are smaller, single-copy DNA is constant within each suborder, and differences in repetitive DNA involve fractions that become increasingly heterogeneous with widening phylogenetic distance. With regard to variation in karyotype morphology, turtles and crocodiles show low variability in chromosome number, morphology, and G-banding pattern. Greater variability is found among squamates, which have a similar degree of karyotypic change-as do some mammals, such as carnivores and bats-and in which there are also differences among congeneric species. An interesting relationship has been highlighted in the entire class Reptilia between rates of change in chromosomes, number of living species, and rate of extinction. However, different situations obtain in turtles and crocodiles on the one hand, and squamates on the other. In the former, the rate of change in chromosomes is lower and the various evolutionary steps do not seem to have entailed marked chromosomal variation, whereas squamates have a higher rate of change in chromosomes clearly related to the number of living species, and chromosomal variation seems to have played an important role in the evolution of several taxa. The different evolutionary trends in chromosomes observed between turtles and crocodiles on the one hand and squamates on the other might depend on their different patterns of G-banding.
Collapse
Affiliation(s)
- Ettore Olmo
- Istituto di Biologia e Genetica, Università Politecnica delle Marche and Istituto Nazionale di Biosistemi e Biostrutture, Via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
13
|
Lin CH, Bourque G, Tan P. A comparative synteny map of Burkholderia species links large-scale genome rearrangements to fine-scale nucleotide variation in prokaryotes. Mol Biol Evol 2007; 25:549-58. [PMID: 18162473 DOI: 10.1093/molbev/msm282] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome rearrangement events, including inversions and translocations, are frequently observed across related microbial species, but the impact of such events on functional diversity is unclear. To clarify this relationship, we compared 4 members of the Gram-negative Burkholderia family (Burkholderia pseudomallei, Burkholderia mallei, Burkholderia thailandensis, and Burkholderia cenocepacia) and identified a core set of 2,590 orthologs present in all 4 species (metagenes). The metagenes were organized into 255 synteny blocks whose relative order has been altered by a predicted minimum of 242 genome rearrangement events. Functionally, metagenes within individual synteny blocks were often related. The molecular divergence of metagenes adjacent to synteny breakpoints (boundary metagenes) was significantly greater compared with metagenes within blocks, suggesting an association between breakpoint locations and local fine-scale nucleotide alterations. This phenomenon, referred to as boundary element associated divergence, was also observed in Pseudomonas and Shigella, suggesting that this is a common phenomenon in prokaryotes. We also observed preferential localization of species-specific genes and insertion sequence element to synteny breakpoints in Burkholderia. Our results suggest that in prokaryotes, genome rearrangements may influence functional diversity through the enhanced divergence of boundary genes and the creation of foci for acquiring and deleting species-specific genes.
Collapse
Affiliation(s)
- Chi Ho Lin
- Genome Institute of Singapore, Singapore
| | | | | |
Collapse
|
14
|
Goodstadt L, Heger A, Webber C, Ponting CP. An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes. Genome Res 2007; 17:969-81. [PMID: 17495010 PMCID: PMC1899124 DOI: 10.1101/gr.6093907] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chromosomes. Using PhyOP, we have established orthologs in Homo for 82% (15,250) of Monodelphis gene predictions. Those with single orthologs in each species exhibited a high median synonymous substitution rate (d(S) = 1.02), thereby explaining the relative paucity of aligned regions outside of coding sequences. Orthology assignments were used to construct a synteny map that illustrates the considerable fragmentation of Monodelphis and Homo karyotypes since their therian last common ancestor. Fifteen percent of Monodelphis genes are predicted, from their low divergence at synonymous sites, to have been duplicated in the metatherian lineage. The majority of Monodelphis-specific genes possess predicted roles in chemosensation, reproduction, adaptation to specific diets, and immunity. Using alignments of Monodelphis genes to sequences from either Homo or Trichosurus vulpecula (an Australian marsupial), we show that metatherian X chromosomes have elevated silent substitution rates and high G+C contents in comparison with both metatherian autosomes and eutherian chromosomes. Each of these elevations is also a feature of subtelomeric chromosomal regions. We attribute these observations to high rates of female-specific recombination near the chromosomal ends and within the X chromosome, which act to sustain or increase G+C levels by biased gene conversion. In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes.
Collapse
Affiliation(s)
- Leo Goodstadt
- MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Oxford, UK.
| | | | | | | |
Collapse
|
15
|
Marques-Bonet T, Sànchez-Ruiz J, Armengol L, Khaja R, Bertranpetit J, Lopez-Bigas N, Rocchi M, Gazave E, Navarro A. On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees. Genome Biol 2007; 8:R230. [PMID: 17971225 PMCID: PMC2246304 DOI: 10.1186/gb-2007-8-10-r230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2006] [Revised: 10/12/2007] [Accepted: 10/30/2007] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution. RESULTS Contrary to previous findings for this pair of species, we show that genes located in the rearranged chromosomes that differentiate the genomes of humans and chimpanzees, especially genes within rearrangements themselves, present lower divergence than genes elsewhere in the genome. Still, there are considerable differences between individual chromosomes. Chromosome 4, in particular, presents higher divergence in genes located within its rearrangement. CONCLUSION A first conclusion of our analysis is that divergence is lower for genes located in rearranged chromosomes than for those in colinear chromosomes. We also report that non-coding regions within rearranged regions tend to have lower divergence than non-coding regions outside them. These results suggest an association between chromosomal rearrangements and lower non-coding divergence that has not been reported before, even if some chromosomes do not follow this trend and could be potentially associated with a speciation episode. In summary, without excluding it, our results suggest that chromosomal speciation has not been common along the human and chimpanzee lineage.
Collapse
Affiliation(s)
- Tomàs Marques-Bonet
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
| | - Jesús Sànchez-Ruiz
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
| | - Lluís Armengol
- Genes and Disease Program, Center for Genomic Regulation,. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88, 1. 08003 Barcelona. Catalonia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Razi Khaja
- The Center for Applied Genomics. The Hospital for Sick Children. MaRS Centre - East Tower. 101 College Street, Room 14-706. Toronto, Ontario. Canada
| | - Jaume Bertranpetit
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Núria Lopez-Bigas
- Research Unit on Biomedical Informatics of IMIM/UPF. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
| | - Mariano Rocchi
- Dipartimento di Genetica e Microbiologia. Universita di Bari, Bari, Italy
| | - Elodie Gazave
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
| | - Arcadi Navarro
- Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA) and Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra. Parc de Recerca Biomèdica de Barcelona. Plaça Dr. Aiguader 88. 08003 Barcelona. Catalonia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
- Population Genomics Node (GNV8) National Institute for Bioinformatics (INB), Spain
| |
Collapse
|
16
|
Abstract
A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with "hybridisation" between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation.
Collapse
Affiliation(s)
- N H Barton
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh, EH9 3JT, UK
| |
Collapse
|
17
|
Yue Y, Tsend-Ayush E, Grützner F, Grossmann B, Haaf T. Segmental duplication associated with evolutionary instability of human chromosome 3p25.1. Cytogenet Genome Res 2006; 112:202-7. [PMID: 16484773 DOI: 10.1159/000089871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Accepted: 07/11/2005] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) of human bacterial artificial chromosome (BAC) clones to orangutan metaphase spreads localized a breakpoint between human chromosome 3p25.1 and orangutan chromosome 2 to a <30-kb interval. The inversion occurred in a relatively gene-rich region with seven genes within 500 kb. The underlying breakpoint is closely juxtaposed to validated genes, however no functional gene has been disrupted by the evolutionary rearrangement. An approximately 21-kb DNA segment at the 3p25.1 breakpoint region has been duplicated intrachromosomally and interchromosomally to multiple regions in the orangutan and human genomes, providing additional evidence for the role of segmental duplications in hominoid chromosome evolution.
Collapse
Affiliation(s)
- Y Yue
- Institute for Human Genetics, Mainz University School of Medicine, Mainz, Germany
| | | | | | | | | |
Collapse
|
18
|
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SMJ, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005; 438:803-19. [PMID: 16341006 DOI: 10.1038/nature04338] [Citation(s) in RCA: 1698] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/11/2005] [Indexed: 12/12/2022]
Abstract
Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
Collapse
Affiliation(s)
- Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|