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151 results for “chromosome evolution”
Data from: Molecular cytogenetic and genomic insights to chromosomal evolution
This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10–13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ~360 million years ago.
Data from: A new approach to chromosomal evolution in the giant water bug (Heteroptera: Belostomatidae)
The genus Belostoma, known colloquially as 'giant water bugs', presents striking cytogenetic diversity and extensive chromosome variability. Notwithstanding, its karyotype evolution is not well understood. We analyzed eight species of Belostoma (77 samples). The meiotic analysis revealed 2n=14+XY for B. horvathi and B. candidulum; 2n=22+XY for B. cummings; 2n=26+X1X2Y for B. dentatum, B. elongatum, and B. discretum; and 2n=26+X1X2X3Y for B. testacopallidum and B. dilatatum. All species showed holokinetic chromosomes. Based on heterochromatin distribution patterns and 18S rDNA, the species of the genus Belostoma were separated into four groups. The analysis of C0t-1 DNA showed that the repetitive DNA, partly composed of microsatellite DNA, was absent on the Y chromosome. FISH using a microdissected X chromosome in species with simple sex system presents uniform hybridization in the nuclear region corresponding to the X chromosome. Species with multiple systems revealed discrete markings. The present data in conjunction with the existing literature led us to propose a new evolutionary hypothesis for the group, with an ancestral karyotype with a low diploid number, simple sex determination system, and Nucleolus Organizer Regions (NORs) on the sex chromosomes. That karyotype would have originated other karyotypes through agmatoploidy, simploidy, heterochromatinization, and movement of the 18S rDNA.
Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation". Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated chromosome rearrangements. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, chromosome rearrangements impact multiple cellular processes and these effects need to be considered together, along with those of genic divergence. Understanding the effects of chromosome rearrangements together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
Data from: The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae)
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.
Data from: Analysis of the karyotype structure in Ricolla quadrispinosa (Linneus, 1767): inferences about the chromosomal evolution of the tribes of Harpactorinae (Heteroptera, Reduviidae)
The subfamily Harpactorinae is composed of six tribes. Phylogenetic studies bring together some of Harpactorinae tribes, but by and large the data on evolutionary relationships of the subfamily are scarce. Chromosome studies are of great importance for understanding the systematics of different groups of insects. For Harpactorinae, these studies are restricted to some subfamilies and involved only conventional chromosome analysis. This work analyzed cytogenetically Ricolla quadrispinosa (Linneus, 1767). The chromosome number was determined as 2n = 24 + X1X2Y in males. In metaphase II the autosomal chromosomes were organized in a ring with the pseudo-trivalent of sex chromosomes in its center. After C-banding followed by staining with DAPI, AT-rich blocks in autosomes were observed and the negatively heteropycnotic sex chromosomes. The data obtained, together with existing data for other species of the group, indicated that different chromosomal rearrangements are involved in the evolution of the species. In addition, a proposal of karyotype evolution for the subfamily, based on existing phylogenetic studies for the group is presented.
Data from: A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach
Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE's accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.
Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution
The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.
Karyotype diversification and evolution in Silene (Caryophyllaceae) representatives with sex chromosomes: taxonomic and biogeographical implications
Open the record for dataset details and reuse information.
Figure 4 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 4. Fluorescence in situ hybridization of the (TTAGG)n telomere probe (red signals) in meiotic chromosomes of five Ommexechinae species, counterstained with DAPI (blue). Rearranged chromosomes with are indicated for Ca. maculosa (A), O. macropterum (B), O. virens (C), Cl. bimaculata (D), P. signata (E). Bar = 10µm.
Figure 3 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 3. Fluorescence in situ hybridization of multigene families in mitotic and meiotic chromosomes of five Ommexechinae species, counterstained with DAPI (blue). Chromosomes with positive signals for 18S rDNA (A–E), 5S rDNA (F–J), U2 snDNA (K–O) and H3 (P–T) probes are indicated in white for Ca. maculosa (A, F, K, P), O. macropterum (B, G, L, Q), O. virens (C, H, M, R), Cl. bimaculata (D, I, N, S) and P. signata (E, J, O T). Meiotic cells are presented in most species, except for O. macropterum (B, G, L) and O. virens (H), in which mitotic cells are presented. H3 FISH experiment was unsuccessful in O. macropterum, due to lack of material (Q). Bar = 10µm.
Figure 6 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 6. Schematic representation of two pathways in Ommexechinae L1 autosome evolution. To explain the variable L1 morphology and the distal U2 snDNA location, at least two different inversions must be considered. In the first hypothesis (A), two pericentric inversions are considered, the first one (A1–2) modifying L1 morphology (from acrocentric to submetacentric) and U2 snDNA location (from interstitial to distal), and the second one (A2–3) restoring the acrocentric morphology in P. signata and Cl. bimaculata. The alternative hypothesis involves two different kinds of inversions (B). First, a paracentric inversion changes U2 location without affecting morphology (B1–2) and, then, a pericentric one only changes L1 morphology (B2–3). Both hypotheses are further explained in the paragraph.
Figure 1 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 1. Conventional analysis of mitotic and meiotic chromosomes of five Ommexechinae species. The karyotypes (A–E) and metaphase I of males (F–J) are shown for Ca. maculosa (A, F), O. macropterum (B, G), O. virens (C, H), Cl. bimaculata (D, I) and P. signata (E, J). Male karyotypes were obtained from spermatogonial cells (A–C, E) or from cells in anaphase I (D). Chromosomes are arranged in decreasing order size, and bi-armed autosomes are indicated in red. Male metaphase I shows (F–J) the first pair of autosomes indicated with arrows and the sex chromosomes with dotted lines. The structure of P. signata neo-X chromosome is indicated with light-blue colour and the neo-Y with orange (E, J). Inset (J) highlight P. signata neo-XY. Bar = 10µm.
Figure 2 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 2. Distribution of heterochromatin and chromatin base-richness in five Ommexechinae species. C banding (A–E), CMA3 (F–J) and DAPI (K–O) staining were performed in Ca. maculosa (A, F, K), O. macropterum (B, G, L), O. virens (C, H, M), Cl. bimaculata (D, I, N) and P. signata (E, J, O). Pictures were obtained from female somatic mitosis, in exception to CMA3 and DAPI for P. signata (J, O), in which spermatogonial mitosis is presented, and also in (E, inset), in which C-banding pattern is shown for neo-sex bivalent at metaphase I. Autosomes with positive signals for each technique are indicated with black and white arrows and dotted lines. Yellow arrowheads exemplify the centromeric positive pattern for different banding techniques: C-positive (D), CMA3 positive (I), and DAPI positive (L). The red arrowhead exemplifies additional interstitial C positive blocks (C). Neo-sex chromosomes and their positive signals are indicated green (neo-X) and orange (neo-Y). Insets show in detail the banding patterns of chromosomes of S group in O. macropterum (B) and O. virens (C), and P. signata neo-XY (E, J, O). C = centromere, bar = 10µm except indicated otherwise.
Figure 5 in New insights into the six decades of Mesa's hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea)
Figure 5. Schematic representation of multigene families chromosomal locations. Species names, probes and chromosome numbers are indicated in each figure. Coloured arrowheads show chromosomes that shared probe locations for at least three species and, therefore, homeology is suggested, as follows: L1 chromosomes of all species (U2 snDNA), L2 (5S rDNA location plus H3 in some cases) of P. signata, Cl. bimaculata, O. virens and Ca. maculosa, M3 of Cl. bimaculata, Ca. maculosa, O. virens and O. macropterum (5S rDNA) and X chromosomes of Cl. bimaculata, Ca. maculosa together with XR of P. signata (18S rDNA).
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization
<p>Data generated using <a href="https://gitlab.inria.fr/tgrohens/evotsc">EvoTSC</a> and used in the <a href="https://doi.org/10.24072/pci.mcb.100198">Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization</a> paper.</p> <p>This data is also used in Chapter 5 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Supplementary material 1 from: Di-Nizo CB, Banci KRS, Sato-Kuwabara Y, Silva MJJ (2017) Advances in cytogenetics of Brazilian rodents: cytotaxonomy, chromosome evolution and new karyotypic data. Comparative Cytogenetics 11(4): 833-892. https://doi.org/10.3897/CompCytogen.v11i4.19925
Table S1 : Explanation note: Sequences analysed for phylogenetic reconstruction (Maximum likelihood and Bayesian Inference) of Neacomys, with species, GenBank and lab/ field number, diploid and fundamental number (when available), locality and reference.
Data from: Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis
Transitions in sexual system and reproductive mode may affect the course of sex chromosome evolution, for instance by altering the strength of sexually antagonistic selection. However, there have been few studies of sex chromosomes in systems where such transitions have been documented. The European tadpole shrimp, Triops cancriformis, has undergone a transition from dioecy to androdioecy (a sexual system where hermaphrodites and males coexist), offering an excellent opportunity to test the impact of this transition on the evolution of sex chromosomes. To identify sex-linked markers, to understand mechanisms of sex determination and to investigate differences between sexual systems, we carried out a genome-wide association study using restriction site-associated DNA sequencing (RAD-seq) of 47 males, females and hermaphrodites from one dioecious and one androdioecious population. We analysed 22.9 Gb of paired-end sequences and identified and scored >3000 high coverage novel genomic RAD markers. Presence–absence of markers, single-nucleotide polymorphism association and read depth identified 52 candidate sex-linked markers. We show that sex is genetically determined in T. cancriformis, with a ZW system conserved across dioecious and androdioecious populations and that hermaphrodites have likely evolved from females. We also show that the structure of the sex chromosomes differs strikingly, with a larger sex-linked region in the dioecious population compared with the androdioecious population.
Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
<p><span>The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes that likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the <em>Hox</em> gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.</span></p>
Detecting Minimal Residual Diseases (MRD) and Monitoring Clonal Evolution Using Ultrasensitive Chromosomal Aberrations Detection (UCAD) in Multiple Myeloma
ClinicalTrials.gov study NCT06302699. IPD Sharing: NO. Countries: 1. Publications: 1.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.