Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.1
3.5
Journals
Genes
Special Issues
Mechanisms Driving Karyotype Evolution and Genomic Architecture
share announcement

Mechanisms Driving Karyotype Evolution and Genomic Architecture

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (29 February 2020) | Viewed by 68478

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Aurora Ruiz-Herrera

E-Mail Website
Guest Editor
1. Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
2. Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, 08193 Cerdanyola del Vallès, Spain
Interests: comparative and functional genomics; 3D genomics; chromosome evolution; meiosis; speciation
Dr. Marta Farré-Belmonte

E-Mail Website
Guest Editor
School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
Interests: comparative genomics; genome evolution; chromosome dynamics

Special Issue Information

Dear Colleagues,

Understanding the origin of species diversity and their adaptation to a changing environment is one of the most intriguing questions in biology. This diversity is also reflected when looking at how genomes are organized into chromosomes, where significant variation in chromosomal number is observed among vertebrates. Large-scale chromosomal changes such as inversions, translocations, fusions, and fissions, contribute to the reshuffling of genomes, thus, providing new chromosomal forms that natural selection can act upon. Unveiling the genetic and mechanistic basis of these processes will provide insights into how biodiversity originates and is maintained.

To provide a unified and encompassing view of how genomes are organized and regulated a multidisciplinary approach is much needed. This would include, among other approaches, the use of recent technological advancements in genomics and cytogenetics, ranging from microscopy to next-generation sequencing. All in all, with the aim to understand genome plasticity and evolution. In this Special Issue, we would like to invite submissions of original research or review articles on any topic related to the mechanisms of driving karyotype evolution and genomic architecture. From the chromosomal characterization of species to the study of genome function and epigenetics, including the dissection of centromeric and telomeric structures as drivers of evolution, sex chromosomes, and the spatial chromosome organization in somatic and germ cells.

Prof. Aurora Ruiz-Herrera
Dr. Marta Farré-Belmonte
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genome evolution
  • Genome architecture
  • Cytogenomics
  • Chromosome
  • Chromosomal rearrangements
  • Speciation
  • Chromatin

Published Papers (15 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Editorial

Jump to: Research, Review, Other

5 pages, 195 KiB  
Editorial
The Plasticity of Genome Architecture
by Marta Farré and Aurora Ruiz-Herrera
Genes 2020, 11(12), 1413; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121413 - 27 Nov 2020
Cited by 1 | Viewed by 1787
Abstract
Understanding the origin of species and their adaptability to new environments is one of the main questions in biology [...] Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)

Research

Jump to: Editorial, Review, Other

15 pages, 3355 KiB  
Article
Spatial and Temporal Dynamics of Contact Zones Between Chromosomal Races of House Mice, Mus musculus domesticus, on Madeira Island
by Joaquim T. Tapisso, Sofia I. Gabriel, Ana Mota Cerveira, Janice Britton-Davidian, Guila Ganem, Jeremy B. Searle, Maria da Graça Ramalhinho and Maria da Luz Mathias
Genes 2020, 11(7), 748; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11070748 - 06 Jul 2020
Cited by 3 | Viewed by 2563
Abstract
Analysis of contact zones between parapatric chromosomal races can help our understanding of chromosomal divergence and its influence on the speciation process. Monitoring the position and any movement of contact zones can allow particular insights. This study investigates the present (2012–2014) and past [...] Read more.
Analysis of contact zones between parapatric chromosomal races can help our understanding of chromosomal divergence and its influence on the speciation process. Monitoring the position and any movement of contact zones can allow particular insights. This study investigates the present (2012–2014) and past (1998–2002) distribution of two parapatric house mouse chromosomal races—PEDC (Estreito da Calheta) and PADC (Achadas da Cruz)—on Madeira Island, aiming to identify changes in the location and width of their contact. We also extended the 1998–2002 sampling area into the range of another chromosomal race—PLDB (Lugar de Baixo). Clinal analysis indicates no major geographic alterations in the distribution and chromosomal characteristics of the PEDC and PADC races but exhibited a significant shift in position of the Rb (7.15) fusion, resulting in the narrowing of the contact zone over a 10+ year period. We discuss how this long-lasting contact zone highlights the role of landscape on mouse movements, in turn influencing the chromosomal characteristics of populations. The expansion of the sampling area revealed new chromosomal features in the north and a new contact zone in the southern range involving the PEDC and PLDB races. We discuss how different interacting mechanisms (landscape resistance, behaviour, chromosomal incompatibilities, meiotic drive) may help to explain the pattern of chromosomal variation at these contacts between chromosomal races. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

15 pages, 3883 KiB  
Article
A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes)
by Rafael Kretschmer, Ivanete de Oliveira Furo, Anderson José Baia Gomes, Lucas G. Kiazim, Ricardo José Gunski, Analía del Valle Garnero, Jorge C. Pereira, Malcolm A. Ferguson-Smith, Edivaldo Herculano Corrêa de Oliveira, Darren K. Griffin, Thales Renato Ochotorena de Freitas and Rebecca E. O’Connor
Genes 2020, 11(6), 632; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11060632 - 08 Jun 2020
Cited by 7 | Viewed by 3604
Abstract
The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68–86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) [...] Read more.
The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68–86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

20 pages, 2420 KiB  
Article
Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae)
by Alexandr Sember, Šárka Pelikánová, Marcelo de Bello Cioffi, Vendula Šlechtová, Terumi Hatanaka, Hiep Do Doan, Martin Knytl and Petr Ráb
Genes 2020, 11(5), 479; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050479 - 28 Apr 2020
Cited by 8 | Viewed by 3477
Abstract
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping [...] Read more.
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping of multigene families and telomeric repeats. Both species shared (i) a diploid chromosome number 2n = 48 and the karyotype structure, (ii) low amount of constitutive heterochromatin, (iii) the absence of interstitial telomeric sites (ITSs), (iv) a single pair of 5S rDNA loci adjacent to one major rDNA cluster, and (v) a single pair of co-localized U1/U2 snDNA tandem repeats. Both species, on the other hand, differed in (i) the presence/absence of remarkable interstitial block of constitutive heterochromatin on the largest acrocentric pair 11 and (ii) the number of major (CMA3-positive) rDNA sites. Additionally, we applied here, for the first time, the conventional cytogenetics in H. harmandi, a species considered extinct in the wild and/or extensively cross-hybridized with H. molitrix. Its 2n and karyotype description match those found in the previous two species, while silver staining showed differences in distribution of major rDNA. The bighead carps thus represent another case of taxonomic diversity not associated with gross karyotype differentiation, where 2n and karyotype structure cannot help in distinguishing between genomes of closely related species. On the other hand, we demonstrated that two cytogenetic characters (distribution of constitutive heterochromatin and major rDNA) may be useful for diagnosis of pure species. The universality of these markers must be further verified by analyzing other pure populations of bighead carps. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

17 pages, 4716 KiB  
Article
Meiotic Chromosome Contacts as a Plausible Prelude for Robertsonian Translocations
by Sergey Matveevsky, Oxana Kolomiets, Aleksey Bogdanov, Elena Alpeeva and Irina Bakloushinskaya
Genes 2020, 11(4), 386; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040386 - 02 Apr 2020
Cited by 15 | Viewed by 3480
Abstract
Robertsonian translocations are common chromosomal alterations. Chromosome variability affects human health and natural evolution. Despite the significance of such mutations, no mechanisms explaining the emergence of such translocations have yet been demonstrated. Several models have explored possible changes in interphase nuclei. Evidence for [...] Read more.
Robertsonian translocations are common chromosomal alterations. Chromosome variability affects human health and natural evolution. Despite the significance of such mutations, no mechanisms explaining the emergence of such translocations have yet been demonstrated. Several models have explored possible changes in interphase nuclei. Evidence for non-homologous chromosomes end joining in meiosis is scarce, and is often limited to uncovering mechanisms in damaged cells only. This study presents a primarily qualitative analysis of contacts of non-homologous chromosomes by short arms, during meiotic prophase I in the mole vole, Ellobius alaicus, a species with a variable karyotype, due to Robertsonian translocations. Immunocytochemical staining of spermatocytes demonstrated the presence of four contact types for non-homologous chromosomes in meiotic prophase I: (1) proximity, (2) touching, (3) anchoring/tethering, and (4) fusion. Our results suggest distinct mechanisms for chromosomal interactions in meiosis. Thus, we propose to change the translocation mechanism model from ‘contact first’ to ‘contact first in meiosis’. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

17 pages, 1207 KiB  
Article
Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism
by Svetlana A. Romanenko, Antonina V. Smorkatcheva, Yulia M. Kovalskaya, Dmitry Yu. Prokopov, Natalya A. Lemskaya, Olga L. Gladkikh, Ivan A. Polikarpov, Natalia A. Serdyukova, Vladimir A. Trifonov, Anna S. Molodtseva, Patricia C. M. O’Brien, Feodor N. Golenishchev, Malcolm A. Ferguson-Smith and Alexander S. Graphodatsky
Genes 2020, 11(4), 374; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040374 - 30 Mar 2020
Cited by 7 | Viewed by 3940
Abstract
The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the [...] Read more.
The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

20 pages, 4117 KiB  
Article
Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex
by Atashi Sharma, Nicholas A. Kinney, Vladimir A. Timoshevskiy, Maria V. Sharakhova and Igor V. Sharakhov
Genes 2020, 11(3), 327; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030327 - 19 Mar 2020
Cited by 13 | Viewed by 3868
Abstract
Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, [...] Read more.
Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, and An. quadriannulatus. Using fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes of An. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation, An. arabiensis, An. merus, An. quadriannulatus, and An. coluzzii or An. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in speciation of mosquitoes. We found that An. coluzzii and An. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

12 pages, 2165 KiB  
Article
Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: Aramides cajaneus and Psophia viridis
by Ivanete de Oliveira Furo, Rafael Kretschmer, Patrícia C. M. O’Brien, Jorge C. Pereira, Malcolm A. Ferguson-Smith and Edivaldo Herculano Corrêa de Oliveira
Genes 2020, 11(3), 307; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030307 - 13 Mar 2020
Cited by 8 | Viewed by 2454
Abstract
Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by [...] Read more.
Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

13 pages, 1353 KiB  
Article
Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae)
by Francisca Garcia, Luis Biedma, Javier Calzada, Jacinto Román, Alberto Lozano, Francisco Cortés, José A. Godoy and Aurora Ruiz-Herrera
Genes 2020, 11(3), 270; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030270 - 02 Mar 2020
Cited by 1 | Viewed by 2802
Abstract
The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is [...] Read more.
The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

14 pages, 2290 KiB  
Article
Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective
by Alexandr Sember, Ezequiel Aguiar de Oliveira, Petr Ráb, Luiz Antonio Carlos Bertollo, Natália Lourenço de Freitas, Patrik Ferreira Viana, Cassia Fernanda Yano, Terumi Hatanaka, Manoela Maria Ferreira Marinho, Renata Luiza Rosa de Moraes, Eliana Feldberg and Marcelo de Bello Cioffi
Genes 2020, 11(1), 91; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11010091 - 13 Jan 2020
Cited by 15 | Viewed by 3445
Abstract
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability [...] Read more.
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

14 pages, 2768 KiB  
Article
Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species
by Anastasia A. Proskuryakova, Anastasia I. Kulemzina, Polina L. Perelman, Dmitry V. Yudkin, Natalya A. Lemskaya, Innokentii M. Okhlopkov, Egor V. Kirillin, Marta Farré, Denis M. Larkin, Melody E. Roelke-Parker, Stephen J. O’Brien, Mitchell Bush and Alexander S. Graphodatsky
Genes 2019, 10(11), 857; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10110857 - 29 Oct 2019
Cited by 8 | Viewed by 5791
Abstract
Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we [...] Read more.
Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirk’s Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB1. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

Review

Jump to: Editorial, Research, Other

16 pages, 1047 KiB  
Review
Turtle Insights into the Evolution of the Reptilian Karyotype and the Genomic Architecture of Sex Determination
by Basanta Bista and Nicole Valenzuela
Genes 2020, 11(4), 416; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11040416 - 11 Apr 2020
Cited by 36 | Viewed by 6458
Abstract
Sex chromosome evolution remains an evolutionary puzzle despite its importance in understanding sexual development and genome evolution. The seemingly random distribution of sex-determining systems in reptiles offers a unique opportunity to study sex chromosome evolution not afforded by mammals or birds. These reptilian [...] Read more.
Sex chromosome evolution remains an evolutionary puzzle despite its importance in understanding sexual development and genome evolution. The seemingly random distribution of sex-determining systems in reptiles offers a unique opportunity to study sex chromosome evolution not afforded by mammals or birds. These reptilian systems derive from multiple transitions in sex determination, some independent, some convergent, that lead to the birth and death of sex chromosomes in various lineages. Here we focus on turtles, an emerging model group with growing genomic resources. We review karyotypic changes that accompanied the evolution of chromosomal systems of genotypic sex determination (GSD) in chelonians from systems under the control of environmental temperature (TSD). These transitions gave rise to 31 GSD species identified thus far (out of 101 turtles with known sex determination), 27 with a characterized sex chromosome system (13 of those karyotypically). These sex chromosomes are varied in terms of the ancestral autosome they co-opted and thus in their homology, as well as in their size (some are macro-, some are micro-chromosomes), heterogamety (some are XX/XY, some ZZ/ZW), dimorphism (some are virtually homomorphic, some heteromorphic with larger-X, larger W, or smaller-Y), age (the oldest system could be ~195 My old and the youngest < 25 My old). Combined, all data indicate that turtles follow some tenets of classic theoretical models of sex chromosome evolution while countering others. Finally, although the study of dosage compensation and molecular divergence of turtle sex chromosomes has lagged behind research on other aspects of their evolution, this gap is rapidly decreasing with the acceleration of ongoing research and growing genomic resources in this group. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

21 pages, 6072 KiB  
Review
Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair
by Sandra Louzada, Mariana Lopes, Daniela Ferreira, Filomena Adega, Ana Escudeiro, Margarida Gama-Carvalho and Raquel Chaves
Genes 2020, 11(1), 72; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11010072 - 09 Jan 2020
Cited by 44 | Viewed by 7866
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. [...] Read more.
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

17 pages, 934 KiB  
Review
Chromosomics: Bridging the Gap between Genomes and Chromosomes
by Janine E. Deakin, Sally Potter, Rachel O’Neill, Aurora Ruiz-Herrera, Marcelo B. Cioffi, Mark D.B. Eldridge, Kichi Fukui, Jennifer A. Marshall Graves, Darren Griffin, Frank Grutzner, Lukáš Kratochvíl, Ikuo Miura, Michail Rovatsos, Kornsorn Srikulnath, Erik Wapstra and Tariq Ezaz
Genes 2019, 10(8), 627; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10080627 - 20 Aug 2019
Cited by 71 | Viewed by 12039
Abstract
The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised [...] Read more.
The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term ‘chromosomics’ as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

Other

13 pages, 438 KiB  
Opinion
Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes
by Homa Papoli Yazdi, Willian T. A. F. Silva and Alexander Suh
Genes 2020, 11(10), 1153; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101153 - 30 Sep 2020
Cited by 7 | Viewed by 3706
Abstract
The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive [...] Read more.
The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds. Full article
(This article belongs to the Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-15
Back to TopTop