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Alves Barcellos S, Kretschmer R, Santos de Souza M, Tura V, Pozzobon LC, Ochotorena de Freitas TR, Griffin DK, O'Connor R, Gunski RJ, Del Valle Garnero A. Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis. Genome 2024. [PMID: 38742652 DOI: 10.1139/gen-2023-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.
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Affiliation(s)
- Suziane Alves Barcellos
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Victoria Tura
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Luciano Cesar Pozzobon
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Thales Renato Ochotorena de Freitas
- Departamento de Genética, Laboratório de Citogenética e Evolução, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil
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Setti PG, Deon GA, Zeni Dos Santos R, Goes CAG, Garnero ADV, Gunski RJ, de Oliveira EHC, Porto-Foresti F, de Freitas TRO, Silva FAO, Liehr T, Utsunomia R, Kretschmer R, de Bello Cioffi M. Evolution of bird sex chromosomes: a cytogenomic approach in Palaeognathae species. BMC Ecol Evol 2024; 24:51. [PMID: 38654159 PMCID: PMC11036779 DOI: 10.1186/s12862-024-02230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa). RESULTS From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu's sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats. CONCLUSION The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.
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Affiliation(s)
- Príncia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | | | | | - Analía Del Valle Garnero
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - Fábio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | | | - Fábio Augusto Oliveira Silva
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, 07747, Jena, Germany.
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, 96.010-610, Pelotas, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
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3
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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa). DIVERSITY 2022. [DOI: 10.3390/d14121068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.
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5
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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6
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The Length Polymorphism of the 9th Intron in the Avian CHD1 Gene Allows Sex Determination in Some Species of Palaeognathae. Genes (Basel) 2022; 13:genes13030507. [PMID: 35328061 PMCID: PMC8954394 DOI: 10.3390/genes13030507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
In palaeognathous birds, several PCR-based methods and a range of genes and unknown genomic regions have been studied for the determination of sex. Many of these methods have proven to be unreliable, complex, expensive, and time-consuming. Even the most widely used PCR markers for sex typing in birds, the selected introns of the highly conserved CHD1 gene (primers P2/P8, 1237L/1272H, and 2550F/2718R), have rarely been effective in palaeognathous birds. In this study we used eight species of Palaeognathae to test three PCR markers: CHD1i9 (CHD1 gene intron 9) and NIPBLi16 (NIPBL gene intron 16) that performed properly as Psittaciformes sex differentiation markers, but have not yet been tested in Palaeognathae, as well as the CHD1iA intron (CHD1 gene intron 16), which so far has not been used effectively to sex palaeognathous birds. The results of our research indicate that the CHD1i9 marker effectively differentiates sex in four of the eight species we studied. In Rhea americana, Eudromia elegans, and Tinamus solitarius, the electrophoretic patterns of the amplicons obtained clearly indicate the sex of tested individuals, whereas in Crypturellus tataupa, sexing is possible based on poorly visible female specific bands. Additionally, we present and discuss the results of our in silico investigation on the applicability of CHD1i9 to sex other Palaeognathae that were not tested in this study.
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7
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots. Nat Commun 2022; 13:944. [PMID: 35177601 PMCID: PMC8854603 DOI: 10.1038/s41467-022-28585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots. Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.
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8
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Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
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9
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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: 57] [Impact Index Per Article: 19.0] [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.
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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
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10
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Okuno M, Mizushima S, Kuroiwa A, Itoh T. Analysis of Sex Chromosome Evolution in the Clade Palaeognathae from Phased Genome Assembly. Genome Biol Evol 2021; 13:6413640. [PMID: 34718546 PMCID: PMC8599748 DOI: 10.1093/gbe/evab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Birds in the clade Palaeognathae, excluding Tinamiformes, have morphologically conserved karyotypes and less differentiated ZW sex chromosomes compared with those of other birds. In particular, the sex chromosomes of the ostrich and emu have exceptionally large recombining pseudoautosomal regions (PARs), whereas non-PARs are classified into two strata according to the date of their origins: stratum 0 and stratum 1 (S1). However, the construction and analysis of the genome sequences in these regions in the clade Palaeognathae can be challenging because assembling the S1 region is difficult owing to low sequence diversity between gametologs (Z-linked and W-linked sequences). We addressed this issue by applying the Platanus-allee assembler and successfully constructed the haplotype-resolved (phased) assembly for female emu, cassowary, and ostrich using only sequence read data derived from the Illumina platform. Comparative genomic and phylogenetic analyses based on assembled Z-linked and W-linked sequences confirmed that the S1 region of emu and cassowary formed in their common ancestor. Moreover, the interspersed repetitive sequence landscapes in the S1 regions of female emu showed an expansion of younger repetitive elements in the W-linked S1 region, suggesting an interruption in homologous recombination in the S1 region. These results provide novel insights into the trajectory of sex chromosome evolution in the clade Palaeognathae and suggest that the Illumina-based phased assembly method is an effective approach for elucidating the evolutionary process underlying the transition from homomorphic to differentiated sex chromosomes.
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Affiliation(s)
- Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Shusei Mizushima
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Asato Kuroiwa
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
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11
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Profile of Jennifer Marshall Graves. Proc Natl Acad Sci U S A 2021; 118:2116850118. [PMID: 34686610 DOI: 10.1073/pnas.2116850118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
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12
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Jiang H, Lin JQ, Sun L, Xu YC, Fang SG. Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei ( Garrulax canorus). Genes (Basel) 2021; 12:genes12040569. [PMID: 33919806 PMCID: PMC8070764 DOI: 10.3390/genes12040569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
It is common that males and females display sexual dimorphisms, which usually result from sex-biased gene expression. Chinese hwamei (Garrulax canorus) is a good model for studying sex-biased gene expression because the song between the sexes is quite different. In this study, we analyze cerebrum and syrinx sex-biased gene expression and evolution using the de novo assembled Chinese hwamei transcriptome. In both the cerebrum and syrinx, our study revealed that most female-biased genes were actively expressed in females only, while most male-biased genes were actively expressed in both sexes. In addition, both male- and female-biased genes were enriched on the putative Z chromosome, suggesting the existence of sexually antagonistic genes and the insufficient dosage compensation of the Z-linked genes. We also identified a 9 Mb sex linkage region on the putative 4A chromosome which enriched more than 20% of female-biased genes. Resultantly, male-biased genes in both tissues had significantly higher Ka/Ks and effective number of codons (ENCs) than unbiased genes, and this suggested that male-biased genes which exhibit accelerated divergence may have resulted from positive selection. Taken together, our results initially revealed the reasons for the differences in singing behavior between males and females of Chinese hwamei.
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Affiliation(s)
- Hua Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Li Sun
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Yan-Chun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China;
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation, Harbin 150040, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
- Correspondence: ; Tel.: +86-571-88206472
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13
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Mazzoleni S, Němec P, Albrecht T, Lymberakis P, Kratochvíl L, Rovatsos M. Long-term stability of sex chromosome gene content allows accurate qPCR-based molecular sexing across birds. Mol Ecol Resour 2021; 21:2013-2021. [PMID: 33720488 DOI: 10.1111/1755-0998.13381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/13/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
Embryos, juveniles, and even adults of many bird species lack pronounced external sexually dimorphic characteristics. Accurate identification of sex is crucial for research (e.g., developmental, population, and evolutionary studies), management of wildlife species, and captive breeding programmes for both conservation and poultry. An accurate molecular sexing method applicable across the entire bird radiation is theoretically possible thanks to the long-term stability of their ZZ/ZW sex chromosomes, but current methods are not applicable in a wide range of bird lineages. Here, we developed a novel molecular sexing method based on the comparison of gene copy number variation by quantitative real-time PCR (qPCR) in conserved Z-specific genes (CHRNA6, DDX4, LPAR1, TMEM161B, VPS13A), i.e. genes linked to Z but absent from W chromosomes. We tested the method across three paleognath and 70 neognath species covering the avian phylogeny. In addition, we designed primers for four Z-specific genes (DOCK8, FUT10, PIGG and PSD3) for qPCR-based molecular sexing in three paleognath species. We have demonstrated that the genes DOCK8, FUT10, PIGG and PSD3 can identify sex in paleognath birds and the genes CHRNA6, DDX4, TMEM161B, and VPS13A can reveal sex in neognath birds. The gene LPAR1 can be used to accurately identify sex in both paleognath and neognath species. Along with outlining a novel method of practical importance for molecular sexing in birds, our study also documents in detail the conservation of sex chromosomes across the avian phylogeny.
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Affiliation(s)
- Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Greece
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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14
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Sanderson BJ, Feng G, Hu N, Carlson CH, Smart LB, Keefover-Ring K, Yin T, Ma T, Liu J, DiFazio SP, Olson MS. Sex determination through X-Y heterogamety in Salix nigra. Heredity (Edinb) 2021; 126:630-639. [PMID: 33510464 PMCID: PMC8115673 DOI: 10.1038/s41437-020-00397-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigra SLR is characterized by strong recombination suppression across a 2 MB region and an excess of low-frequency alleles, resulting in a low Tajima's D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima's D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.
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Affiliation(s)
- Brian J. Sanderson
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA ,grid.268154.c0000 0001 2156 6140Present Address: Department of Biology, West Virginia University, Morgantown, WV 26506-6057 USA
| | - Guanqiao Feng
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
| | - Nan Hu
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
| | - Craig H. Carlson
- grid.5386.8000000041936877XHorticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456 USA
| | - Lawrence B. Smart
- grid.5386.8000000041936877XHorticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456 USA
| | - Ken Keefover-Ring
- grid.14003.360000 0001 2167 3675Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Tongming Yin
- grid.410625.40000 0001 2293 4910Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Jianquan Liu
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu, 610065 China ,grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Stephen P. DiFazio
- grid.268154.c0000 0001 2156 6140Department of Biology, West Virginia University, Morgantown, WV 26506-6057 USA
| | - Matthew S. Olson
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
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15
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Ehl J, Altmanová M, Kratochvíl L. With or Without W? Molecular and Cytogenetic Markers are Not Sufficient for Identification of Environmentally-Induced Sex Reversal in the Bearded Dragon. Sex Dev 2021; 15:272-281. [PMID: 33756476 DOI: 10.1159/000514195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022] Open
Abstract
Transitions from environmental sex determination (ESD) to genotypic sex determination (GSD) require an intermediate step of sex reversal, i.e., the production of individuals with a mismatch between the ancestral genotypic and the phenotypic sex. Among amniotes, the sole well-documented transition in this direction was shown in the laboratory in the central bearded dragon, Pogona vitticeps, where very high incubation temperatures led to the production of females with the male-typical (ZZ) genotype. These sex-reversed females then produced offspring whose sex depended on the incubation temperature. Sex-reversed animals identified by molecular and cytogenetic markers were also reported in the field, and their increasing incidence was speculated as a climate warming-driven transition in sex determination. We show that the molecular and cytogenetic markers normally sex-linked in P. vitticeps are also sex-linked in P. henrylawsoni and P. minor, which points to quite ancient sex chromosomes in this lineage. Nevertheless, we demonstrate, based on a crossing experiment with a male bearded dragon who possesses a mismatch between phenotypic sex and genotype, that the used cytogenetic and molecular markers might not be reliable for the identification of sex reversal. Sex reversal should not be considered as the only mechanism causing a mismatch between genetic sex-linked markers and phenotypic sex, which can emerge also by other processes, here most likely by a rare recombination between regions of sex chromosomes which are normally sex-linked. We warn that sex-linked, even apparently for a long evolutionary time, and sex-specific molecular and cytogenetic markers are not a reliable tool for the identification of sex-reversed individuals in a population and that sex reversal has to be verified by other approaches, particularly by observation of the sex ratio of the progeny.
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Affiliation(s)
- Jan Ehl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia.,Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czechia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia,
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16
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Wang ZJ, Chen GJ, Zhang GJ, Zhou Q. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zool Res 2021; 42:51-61. [PMID: 33124220 PMCID: PMC7840455 DOI: 10.24272/j.issn.2095-8137.2020.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution. Here, we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories, which are presently unknown. We found that most species showed a reduction of population size since the beginning of the last glacial period, except for those species distributed in Australasia and in the far south of South America. Different degrees of contraction and expansion of transposable elements (TE) have shaped the paleognathous genome architecture, with a higher transposon removal rate in tinamous than in ratites. One repeat family, AviRTE, likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago. Our analysis of gene families identified rapid turnover of immune and reproduction-related genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites. We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites, with the former also showing more degenerated W chromosomes. This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria. Overall, we reconstructed the evolutionary history of the Palaeognathae populations, genes, and TEs. Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.
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Affiliation(s)
- Zong-Ji Wang
- Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China.,MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China
| | - Guang-Ji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China
| | - Guo-Jie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria.,Center for Reproductive Medicine, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China. E-mail:
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17
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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18
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Repeat Sequence Mapping Shows Different W Chromosome Evolutionary Pathways in Two Caprimulgiformes Families. BIRDS 2020. [DOI: 10.3390/birds1010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although birds belonging to order Caprimulgiformes show extensive karyotype variation, data concerning their genomic organization is still scarce, as most studies have presented only results obtained from conventional staining analyses. Nevertheless, some interesting findings have been observed, such as the W chromosome of the Common Potoo, Nyctibius griseus (2n = 86), which has the same morphology and size of the Z chromosome, a rare feature in Neognathae birds. Hence, we aimed to investigate the process by which the W chromosome of this species was enlarged. For that, we analyzed comparatively the chromosome organization of the Common Potoo and the Scissor-tailed Nightjar, Hydropsalis torquata (2n = 74), which presents the regular differentiated sex chromosomes, by applying C-banding, G-banding and mapping of repetitive DNAs (microsatellite repeats and 18S rDNA). Our results showed an accumulation of constitutive heterochromatin in the W chromosome of both species. However, 9 out of 11 microsatellite sequences hybridized in the large W chromosome in the Common Potoo, while none of them hybridized in the W chromosome of the Scissor-tailed Nightjar. Therefore, we can conclude that the accumulation of microsatellite sequences, and consequent increase in constitutive heterochromatin, was responsible for the enlargement of the W chromosome in the Common Potoo. Based on these results, we conclude that even though these two species belong to the same order, their W chromosomes have gone through different evolutionary histories, with an extra step of accumulation of repetitive sequences in the Common Potoo.
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19
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Ma S, Liu H, Sun W, Mustafa A, Xi Y, Pu F, Li Y, Han C, Bai L, Hua H. Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds. BMC Evol Biol 2020; 20:85. [PMID: 32664916 PMCID: PMC7362505 DOI: 10.1186/s12862-020-01654-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Background ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds. Results We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution. Conclusions We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.
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Affiliation(s)
- Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China.
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Ahsan Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, P.R. China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Fajun Pu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Yanying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - Lili Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
| | - He Hua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P.R. China
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20
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Cross-Species BAC Mapping Highlights Conservation of Chromosome Synteny across Dragon Lizards (Squamata: Agamidae). Genes (Basel) 2020; 11:genes11060698. [PMID: 32630412 PMCID: PMC7348930 DOI: 10.3390/genes11060698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 01/23/2023] Open
Abstract
Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in Phrynocephalus vlangalii from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon (Pogona vitticeps) are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of P. vitticeps across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of P. vitticeps. We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of P. vitticeps. Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination.
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21
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Xirocostas ZA, Everingham SE, Moles AT. The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life. Biol Lett 2020; 16:20190867. [PMID: 32126186 PMCID: PMC7115182 DOI: 10.1098/rsbl.2019.0867] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/10/2020] [Indexed: 01/02/2023] Open
Abstract
Many taxa show substantial differences in lifespan between the sexes. However, these differences are not always in the same direction. In mammals, females tend to live longer than males, while in birds, males tend to live longer than females. One possible explanation for these differences in lifespan is the unguarded X hypothesis, which suggests that the reduced or absent chromosome in the heterogametic sex (e.g. the Y chromosome in mammals and the W chromosome in birds) exposes recessive deleterious mutations on the other sex chromosome. While the unguarded X hypothesis is intuitively appealing, it had never been subject to a broad test. We compiled male and female longevity data for 229 species spanning 99 families, 38 orders and eight classes across the tree of life. Consistent with the unguarded X hypothesis, a meta-analysis showed that the homogametic sex, on average, lives 17.6% longer than the heterogametic sex. Surprisingly, we found substantial differences in lifespan dimorphism between female heterogametic species (in which the homogametic sex lives 7.1% longer) and male heterogametic species (in which the homogametic sex lives 20.9% longer). Our findings demonstrate the importance of considering chromosome morphology in addition to sexual selection and environment as potential drivers of sexual dimorphism, and advance our fundamental understanding of the mechanisms that shape an organism's lifespan.
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Affiliation(s)
- Zoe A. Xirocostas
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Susan E. Everingham
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
- The Australian PlantBank, Royal Botanic Gardens and Domain Trust, Australian Botanic Garden, Mount Annan, New South Wales 2567, Australia
| | - Angela T. Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
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22
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Nielsen SV, Pinto BJ, Guzmán-Méndez IA, Gamble T. First Report of Sex Chromosomes in Night Lizards (Scincoidea: Xantusiidae). J Hered 2020; 111:307-317. [DOI: 10.1093/jhered/esaa007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Abstract
Squamate reptiles (lizards, snakes, and amphibians) are an outstanding group for studying sex chromosome evolution—they are old, speciose, geographically widespread, and exhibit myriad sex-determining modes. Yet, the vast majority of squamate species lack heteromorphic sex chromosomes. Cataloging the sex chromosome systems of species lacking easily identifiable, heteromorphic sex chromosomes, therefore, is essential before we are to fully understand the evolution of vertebrate sex chromosomes. Here, we use restriction site-associated DNA sequencing (RADseq) to classify the sex chromosome system of the granite night lizard, Xantusia henshawi. RADseq is an effective alternative to traditional cytogenetic methods for determining a species’ sex chromosome system (i.e., XX/XY or ZZ/ZW), particularly in taxa with non-differentiated sex chromosomes. Although many xantusiid lineages have been karyotyped, none possess heteromorphic sex chromosomes. We identified a ZZ/ZW sex chromosome system in X. henshawi—the first such data for this family. Furthermore, we report that the X. henshawi sex chromosome contains fragments of genes found on Gallus gallus chromosomes 7, 12, and 18 (which are homologous to Anolis carolinensis chromosome 2), the first vertebrate sex chromosomes to utilize this linkage group.
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Affiliation(s)
- Stuart V Nielsen
- Florida Museum of Natural History, University of Florida, Gainesville, FL
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | - Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN
- Milwaukee Public Museum, Milwaukee, WI
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23
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Shams F, Dyer F, Thompson R, Duncan RP, Thiem JD, Kilian A, Ezaz T. Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua. PLoS One 2019; 14:e0226365. [PMID: 31830141 PMCID: PMC6907852 DOI: 10.1371/journal.pone.0226365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/25/2019] [Indexed: 01/09/2023] Open
Abstract
Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1–0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.
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Affiliation(s)
- Foyez Shams
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- * E-mail: (FS); (TE)
| | - Fiona Dyer
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- Centre for Applied Water Science, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Ross Thompson
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- Centre for Applied Water Science, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Richard P. Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Jason D. Thiem
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Andrzej Kilian
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- Diversity Arrays Technology, Bruce, Australian Capital Territory, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- * E-mail: (FS); (TE)
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Sigeman H, Ponnikas S, Chauhan P, Dierickx E, Brooke MDL, Hansson B. Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes. Proc Biol Sci 2019; 286:20192051. [PMID: 31771477 PMCID: PMC6939255 DOI: 10.1098/rspb.2019.2051] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/01/2019] [Indexed: 12/28/2022] Open
Abstract
Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that selection for recombination suppression has acted repeatedly and independently on certain genetic backgrounds. Here, we perform comparative genomics of a bird clade (larks and their sister lineage; Alaudidae and Panuridae) where multiple autosome-sex chromosome fusions appear to have formed expanded sex chromosomes. We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between parts of four avian chromosomes: Z, 3, 4A and 5. Within these four chromosomes, we found evidence of five evolutionary strata where recombination had been suppressed at different time points, and show that stratum age explained the divergence rate of Z-W gametologs. Next, we analysed chromosome content and found that chromosome 3 was significantly enriched for genes with predicted sex-related functions. Finally, we demonstrate extensive homology to sex chromosomes in other vertebrate lineages: chromosomes Z, 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5). Our results provide insights into and support for repeated evolution of sex chromosomes in vertebrates.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Elisa Dierickx
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, UK
| | - M. de L. Brooke
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, UK
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
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25
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Iannucci A, Altmanová M, Ciofi C, Ferguson-Smith M, Milan M, Pereira JC, Pether J, Rehák I, Rovatsos M, Stanyon R, Velenský P, Ráb P, Kratochvíl L, Johnson Pokorná M. Conserved sex chromosomes and karyotype evolution in monitor lizards (Varanidae). Heredity (Edinb) 2019; 123:215-227. [PMID: 30670841 PMCID: PMC6781170 DOI: 10.1038/s41437-018-0179-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022] Open
Abstract
Despite their long history with the basal split dating back to the Eocene, all species of monitor lizards (family Varanidae) studied so far share the same chromosome number of 2n = 40. However, there are differences in the morphology of the macrochromosome pairs 5-8. Further, sex determination, which revealed ZZ/ZW sex microchromosomes, was studied only in a few varanid species and only with techniques that did not test their homology. The aim of this study was to (i) test if cryptic interchromosomal rearrangements of larger chromosomal blocks occurred during the karyotype evolution of this group, (ii) contribute to the reconstruction of the varanid ancestral karyotype, and (iii) test homology of sex chromosomes among varanids. We investigated these issues by hybridizing flow sorted chromosome paints from Varanus komodoensis to metaphases of nine species of monitor lizards. The results show that differences in the morphology of the chromosome pairs 5-8 can be attributed to intrachromosomal rearrangements, which led to transitions between acrocentric and metacentric chromosomes in both directions. We also documented the first case of spontaneous triploidy among varanids in Varanus albigularis. The triploid individual was fully grown, which demonstrates that polyploidization is compatible with life in this lineage. We found that the W chromosome differs between species in size and heterochromatin content. The varanid Z chromosome is clearly conserved in all the analyzed species. Varanids, in addition to iguanas, caenophidian snakes, and lacertid lizards, are another squamate group with highly conserved sex chromosomes over a long evolutionary time.
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Affiliation(s)
- Alessio Iannucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marie Altmanová
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Claudio Ciofi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Malcolm Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Jorge Claudio Pereira
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom
| | - James Pether
- Reptilandia Park, Galdar, 35460, Gran Canaria, Spain
| | - Ivan Rehák
- Prague Zoological Garden, U Trojského zámku 120/3, 171 00, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Petr Velenský
- Prague Zoological Garden, U Trojského zámku 120/3, 171 00, Prague, Czech Republic
| | - Petr Ráb
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic.
| | - Martina Johnson Pokorná
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
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26
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Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
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27
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Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species. PLoS One 2019; 14:e0214028. [PMID: 30913221 PMCID: PMC6435179 DOI: 10.1371/journal.pone.0214028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 01/22/2023] Open
Abstract
The highly repetitive DNA sequence of centromeric heterochromatin is an effective molecular cytogenetic marker for investigating genomic compartmentalization between macrochromosomes and microchromosomes in birds. We isolated four repetitive sequence families of centromeric heterochromatin from three Anseriformes species, viz., domestic duck (Anas platyrhynchos, APL), bean goose (Anser fabalis, AFA), and whooper swan (Cygnus cygnus, CCY), and characterized the sequences by molecular cytogenetic approach. The 190-bp APL-HaeIII and 101-bp AFA-HinfI-S sequences were localized in almost all chromosomes of A. platyrhynchos and A. fabalis, respectively. However, the 192-bp AFA-HinfI-L and 290-bp CCY-ApaI sequences were distributed in almost all microchromosomes of A. fabalis and in approximately 10 microchromosomes of C. cygnus, respectively. APL-HaeIII, AFA-HinfI-L, and CCY-ApaI showed partial sequence homology with the chicken nuclear-membrane-associated (CNM) repeat families, which were localized primarily to the centromeric regions of microchromosomes in Galliformes, suggesting that ancestral sequences of the CNM repeat families are observed in the common ancestors of Anseriformes and Galliformes. These results collectively provide the possibility that homogenization of centromeric heterochromatin occurred between microchromosomes in Anseriformes and Galliformes; however, homogenization between macrochromosomes and microchromosomes also occurred in some centromeric repetitive sequences.
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28
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O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 2018; 19:171. [PMID: 30355328 PMCID: PMC6201548 DOI: 10.1186/s13059-018-1550-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/24/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. RESULTS We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. CONCLUSIONS The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
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Affiliation(s)
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Sophie Bennett
- School of Biosciences, University of Kent, Canterbury, UK
| | - Eden A Slack
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Emily Allanson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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29
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Kartout-Benmessaoud Y, Ladjali-Mohammedi K. Banding cytogenetics of chimeric hybrids Coturnixcoturnix × Coturnixjaponica and comparative analysis with the domestic fowl. COMPARATIVE CYTOGENETICS 2018; 12:445-470. [PMID: 30364889 PMCID: PMC6199345 DOI: 10.3897/compcytogen.v12i4.27341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The Common quail Coturnixcoturnix Linnaeus, 1758 is a wild migratory bird which is distributed in Eurasia and North Africa, everywhere with an accelerating decline in population size. This species is protected by the Bonn and Berne conventions (1979) and by annex II/1 of the Birds Directive (2009). In Algeria, its breeding took place at the hunting centre in the west of the country. Breeding errors caused uncontrolled crosses between the Common quail and Japanese quail Coturnixjaponica Temminck & Schlegel, 1849. In order to help to preserve the natural genetic heritage of the Common quail and to lift the ambiguity among the populations of quail raised in Algeria, it seemed essential to begin to describe the chromosomes of this species in the country since no cytogenetic study has been reported to date. Fibroblast cultures from embryo and adult animal were initiated. Double synchronization with excess thymidine allowed us to obtain high resolution chromosomes blocked at prometaphase stage. The karyotype and the idiogram in GTG morphological banding (G-bands obtained with trypsin and Giemsa) corresponding to larger chromosomes 1-12 and ZW pair were thus established. The diploid set of chromosomes was estimated as 2N=78. Cytogenetic analysis of expected hybrid animals revealed the presence of a genetic introgression and cellular chimerism. This technique is effective in distinguishing the two quail taxa. Furthermore, the comparative chromosomal analysis of the two quails and domestic chicken Gallusgallusdomesticus Linnaeus, 1758 has been conducted. Differences in morphology and/or GTG band motifs were observed on 1, 2, 4, 7, 8 and W chromosomes. Neocentromere occurrence was suggested for Common quail chromosome 1 and Chicken chromosomes 4 and W. Double pericentric inversion was observed on the Common quail chromosome 2 while pericentric inversion hypothesis was proposed for Chicken chromosome 8. A deletion on the short arm of the Common quail chromosome 7 was also found. These results suggest that Common quail would be a chromosomally intermediate species between Chicken and Japanese quail. The appearance of only a few intrachromosomal rearrangements that occurred during evolution suggests that the organization of the genome is highly conserved between these three galliform species.
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Affiliation(s)
- Yasmine Kartout-Benmessaoud
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
- University of Bejaia, Faculty of Nature and Life Sciences, Department of Physico-Chemical Biology, 06000, Bejaia, AlgeriaUniversity of BejaiaBejaiaAlgeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
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30
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Yazdi HP, Ellegren H. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biol Evol 2018; 10:2049-2060. [PMID: 30099482 PMCID: PMC6105114 DOI: 10.1093/gbe/evy163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (≈60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.
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Affiliation(s)
- Homa Papoli Yazdi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
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Sex Chromosomes of the Iconic Moth Abraxas grossulariata (Lepidoptera, Geometridae) and Its Congener A. sylvata. Genes (Basel) 2018; 9:genes9060279. [PMID: 29857494 PMCID: PMC6027526 DOI: 10.3390/genes9060279] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 01/28/2023] Open
Abstract
The magpie moth, Abraxas grossulariata, is an iconic species in which female heterogamety was discovered at the beginning of the 20th century. However, the sex chromosomes of this species have not yet been cytologically identified. We describe the sex chromosomes of A. grossulariata and its congener, A. sylvata. Although these species split only around 9.5 million years ago, and both species have the expected WZ/ZZ chromosomal system of sex determination and their sex chromosomes share the major ribosomal DNA (rDNA) representing the nucleolar organizer region (NOR), we found major differences between their karyotypes, including between their sex chromosomes. The species differ in chromosome number, which is 2n = 56 in A. grossularita and 2n = 58 in A. sylvata. In addition, A. grossularita autosomes exhibit massive autosomal blocks of heterochromatin, which is a very rare phenomenon in Lepidoptera, whereas the autosomes of A. sylvata are completely devoid of distinct heterochromatin. Their W chromosomes differ greatly. Although they are largely composed of female-specific DNA sequences, as shown by comparative genomic hybridization, cross-species W-chromosome painting revealed considerable sequence differences between them. The results suggest a relatively rapid molecular divergence of Abraxas W chromosomes by the independent spreading of female-specific repetitive sequences.
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Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting. Genes (Basel) 2018; 9:genes9040181. [PMID: 29584697 PMCID: PMC5924523 DOI: 10.3390/genes9040181] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/08/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.
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Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes. Proc Natl Acad Sci U S A 2018; 115:2794-2799. [PMID: 29483264 PMCID: PMC5856536 DOI: 10.1073/pnas.1717721115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2m version is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2m chromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2m alleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.
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34
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Nielsen SV, Banks JL, Diaz RE, Trainor PA, Gamble T. Dynamic sex chromosomes in Old World chameleons (Squamata: Chamaeleonidae). J Evol Biol 2018; 31:484-490. [DOI: 10.1111/jeb.13242] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 01/04/2023]
Affiliation(s)
- S. V. Nielsen
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
| | - J. L. Banks
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
| | - R. E. Diaz
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
- Natural History Museum of Los Angeles County; Los Angeles CA USA
| | - P. A. Trainor
- Stowers Institute for Medical Research; Kansas City MO USA
- Department of Anatomy and Cell Biology; Medical Center; University of Kansas; Kansas City KS USA
| | - T. Gamble
- Department of Biological Sciences; Marquette University; Milwaukee WI USA
- Bell Museum of Natural History; University of Minnesota; Saint Paul MN USA
- Milwaukee Public Museum; Milwaukee WI USA
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Abstract
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand. Here I describe some of those amazing animals and the insights on genome structure, function, and evolution they have afforded us. I also describe my sometimes-random walk in science and the factors and people who influenced my direction. Being a woman in science is still not easy, and I hope others will find encouragement and empathy in my story.
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Affiliation(s)
- Jennifer A. Marshall Graves
- School of Life Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Australia Institute of Applied Ecology, University of Canberra, ACT 2617, Australia
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36
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Hormonal and thermal induction of sex reversal in the bearded dragon (Pogona vitticeps, Agamidae). ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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37
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Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez-Muñoz ME, Leulier F, Gänzle M, Walter J. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 2017; 41:S27-S48. [DOI: 10.1093/femsre/fux030] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 02/07/2023] Open
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Chung JW. Spot the difference: Solving the puzzle of hidden pictures in the lizard genome for identification of regeneration factors. BMB Rep 2017; 49:249-54. [PMID: 26949021 PMCID: PMC5070703 DOI: 10.5483/bmbrep.2016.49.5.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
All living things share some common life processes, such as growth and reproduction, and have the ability to respond to their environment. However, each type of organism has its own specialized way of managing biological events. Genetic sequences determine phenotypic and physiological traits. Based on genetic information, comparative genomics has been used to delineate the differences and similarities between various genomes, and significant progress has been made in understanding regenerative biology by comparing the genomes of a variety of lower animal models of regeneration, such as planaria, zebra fish, and newts. However, the genome of lizards has been relatively ignored until recently, even though lizards have been studied as an excellent amniote model of tissue regeneration. Very recently, whole genome sequences of lizards have been uncovered, and several attempts have been made to find regeneration factors based on genetic information. In this article, recent advances in comparative analysis of the lizard genome are introduced, and their biological implications and putative applications for regenerative medicine and stem cell biology are discussed. [BMB Reports 2016; 49(5): 249-254]
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Affiliation(s)
- Jin Woong Chung
- Department of Biological Science, Dong-A University, Busan 49315, Korea
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Yano CF, Bertollo LAC, Ezaz T, Trifonov V, Sember A, Liehr T, Cioffi MB. Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae). Heredity (Edinb) 2016; 118:276-283. [PMID: 28000659 DOI: 10.1038/hdy.2016.83] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 11/09/2022] Open
Abstract
The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15-25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.
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Affiliation(s)
- C F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - T Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - V Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - A Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - T Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - M B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Ezaz T, Srikulnath K, Graves JAM. Origin of Amniote Sex Chromosomes: An Ancestral Super-Sex Chromosome, or Common Requirements? J Hered 2016; 108:94-105. [DOI: 10.1093/jhered/esw053] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
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Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. BMC Genomics 2016; 17:410. [PMID: 27230888 PMCID: PMC4882810 DOI: 10.1186/s12864-016-2714-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi). Results Sequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z. Conclusions Our study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2714-2) contains supplementary material, which is available to authorized users.
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Rovatsos M, Vukić J, Altmanová M, Johnson Pokorná M, Moravec J, Kratochvíl L. Conservation of sex chromosomes in lacertid lizards. Mol Ecol 2016; 25:3120-6. [DOI: 10.1111/mec.13635] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Jasna Vukić
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Jiří Moravec
- Department of Zoology; National Museum; Václavské nám. 68 115 79 Prague Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
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Giovannotti M, Trifonov VA, Paoletti A, Kichigin IG, O’Brien PCM, Kasai F, Giovagnoli G, Ng BL, Ruggeri P, Cerioni PN, Splendiani A, Pereira JC, Olmo E, Rens W, Caputo Barucchi V, Ferguson-Smith MA. New insights into sex chromosome evolution in anole lizards (Reptilia, Dactyloidae). Chromosoma 2016; 126:245-260. [DOI: 10.1007/s00412-016-0585-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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Pal A, Vicoso B. The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression. Genome Biol Evol 2015; 7:3259-68. [PMID: 26556591 PMCID: PMC4700948 DOI: 10.1093/gbe/evv215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order. In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order.
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Affiliation(s)
- Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria Center for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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dos Santos MDS, Kretschmer R, Silva FAO, Ledesma MA, O'Brien PCM, Ferguson-Smith MA, Del Valle Garnero A, de Oliveira EHC, Gunski RJ. Intrachromosomal rearrangements in two representatives of the genus Saltator (Thraupidae, Passeriformes) and the occurrence of heteromorphic Z chromosomes. Genetica 2015; 143:535-43. [PMID: 26092368 DOI: 10.1007/s10709-015-9851-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
Abstract
Saltator is a genus within family Thraupidae, the second largest family of Passeriformes, with more than 370 species found exclusively in the New World. Despite this, only a few species have had their karyotypes analyzed, most of them only with conventional staining. The diploid number is close to 80, and chromosome morphology is similar to the usual avian karyotype. Recent studies using cross-species chromosome painting have shown that, although the chromosomal morphology and number are similar to many species of birds, Passeriformes exhibit a complex pattern of paracentric and pericentric inversions in the chromosome homologous to GGA1q in two different suborders, Oscines and Suboscines. Hence, considering the importance and species richness of Thraupidae, this study aims to analyze two species of genus Saltator, the golden-billed saltator (S. aurantiirostris) and the green-winged saltator (S. similis) by means of classical cytogenetics and cross-species chromosome painting using Gallus gallus and Leucopternis albicollis probes, and also 5S and 18S rDNA and telomeric sequences. The results show that the karyotypes of these species are similar to other species of Passeriformes. Interestingly, the Z chromosome appears heteromorphic in S. similis, varying in morphology from acrocentric to metacentric. 5S and 18S probes hybridize to one pair of microchromosomes each, and telomeric sequences produce signals only in the terminal regions of chromosomes. FISH results are very similar to the Passeriformes already analyzed by means of molecular cytogenetics (Turdus species and Elaenia spectabilis). However, the paracentric and pericentric inversions observed in Saltator are different from those detected in these species, an observation that helps to explain the probable sequence of rearrangements. As these rearrangements are found in both suborders of Passeriformes (Oscines and Suboscines), we propose that the fission of GGA1 and inversions in GGA1q have occurred very early after the radiation of this order.
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Affiliation(s)
- Michelly da Silva dos Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, Pará, Brazil
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Opazo JC, Hoffmann FG, Natarajan C, Witt CC, Berenbrink M, Storz JF. Gene turnover in the avian globin gene families and evolutionary changes in hemoglobin isoform expression. Mol Biol Evol 2015; 32:871-87. [PMID: 25502940 PMCID: PMC4379397 DOI: 10.1093/molbev/msu341] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α2β2 protein responsible for blood-O2 transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during approximately 100 My of avian evolution. Most interspecific variation in gene content is attributable to multiple independent inactivations of the α(D)-globin gene, which encodes the α-chain subunit of a functionally distinct Hb isoform (HbD) that is expressed in both embryonic and definitive erythrocytes. Due to consistent differences in O2-binding properties between HbD and the major adult-expressed Hb isoform, HbA (which incorporates products of the α(A)-globin gene), recurrent losses of α(D)-globin contribute to among-species variation in blood-O2 affinity. Analysis of HbA/HbD expression levels in the red blood cells of 122 bird species revealed high variability among lineages and strong phylogenetic signal. In comparison with the homologous gene clusters in mammals, the low retention rate for lineage-specific gene duplicates in the avian globin gene clusters suggests that the developmental regulation of Hb synthesis in birds may be more highly conserved, with orthologous genes having similar stage-specific expression profiles and similar functional properties in disparate taxa.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | | | - Christopher C Witt
- Department of Biology, University of New Mexico Museum of Southwestern Biology, University of New Mexico
| | - Michael Berenbrink
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
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Jones MR, Cheviron ZA, Carling MD. Spatially variable coevolution between a haemosporidian parasite and the MHC of a widely distributed passerine. Ecol Evol 2015; 5:1045-60. [PMID: 25798222 PMCID: PMC4364819 DOI: 10.1002/ece3.1391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/03/2014] [Accepted: 12/12/2014] [Indexed: 12/12/2022] Open
Abstract
The environment shapes host-parasite interactions, but how environmental variation affects the diversity and composition of parasite-defense genes of hosts is unresolved. In vertebrates, the highly variable major histocompatibility complex (MHC) gene family plays an essential role in the adaptive immune system by recognizing pathogen infection and initiating the cellular immune response. Investigating MHC-parasite associations across heterogeneous landscapes may elucidate the role of spatially fluctuating selection in the maintenance of high levels of genetic variation at the MHC. We studied patterns of association between an avian haemosporidian blood parasite and the MHC of rufous-collared sparrows (Zonotrichia capensis) that inhabit environments with widely varying haemosporidian infection prevalence in the Peruvian Andes. MHC diversity peaked in populations with high infection prevalence, although intra-individual MHC diversity was not associated with infection status. MHC nucleotide and protein sequences associated with infection absence tended to be rare, consistent with negative frequency-dependent selection. We found an MHC variant associated with a ∽26% decrease in infection probability at middle elevations (1501-3100 m) where prevalence was highest. Several other variants were associated with a significant increase in infection probability in low haemosporidian prevalence environments, which can be interpreted as susceptibility or quantitative resistance. Our study highlights important challenges in understanding MHC evolution in natural systems, but may point to a role of negative frequency-dependent selection and fluctuating spatial selection in the evolution of Z. capensisMHC.
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Affiliation(s)
- Matthew R Jones
- Department of Zoology and Physiology, Berry Biodiversity Conservation Center, University of Wyoming 1000 E. University Ave., Dept. 4304, Laramie, Wyoming, 82071
| | - Zachary A Cheviron
- Department of Animal Biology, School of Integrative Biology, University of Illinois Urbana-Champaign 505 South Goodwin Ave., Urbana, Illinois, 61801
| | - Matthew D Carling
- Department of Zoology and Physiology, Berry Biodiversity Conservation Center, University of Wyoming 1000 E. University Ave., Dept. 4304, Laramie, Wyoming, 82071
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Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G, Zhou Q. Temporal genomic evolution of bird sex chromosomes. BMC Evol Biol 2014; 14:250. [PMID: 25527260 PMCID: PMC4272511 DOI: 10.1186/s12862-014-0250-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias ('male-driven evolution' effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. CONCLUSIONS In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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Affiliation(s)
- Zongji Wang
- />School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 China
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jilin Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Wei Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Na An
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pei Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Qi Zhou
- />Department of Integrative Biology, University of California, Berkeley, CA94720 USA
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