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BAC clones hybridised to helmeted guinea fowl chromosome 1. The FITC (green) labelled signal represents CH261-107E2 (chicken 1 homolog), the Texas red labelled signal represents CH261-184E5 (chicken 1 homolog).
Source publication
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 bac...
Context in source publication
Citations
... Thus, although mobilome refers to all transposable elements within a genome, here we have focused the analysis on the LTR-RTs, which, as is the case in most flowering plants, was the overall most abundant mobilome fraction within our Rhynchospora sampling. Because they are in general scattered through the genome, repetitive A c c e p t e d M a n u s c r i p t elements, especially TEs, are often related to driving forces of speciation, such as differentiation between chromosomes and chromosomal regions as well as in chromosomal rearrangements (Chen et al., 2020;Kiazim et al., 2021;Oliveira da Silva et al., 2020). In the holocentric chromosomes of Rhynchospora, however, repetitive elements, including LTR-RTs and the centromeric satDNA Tyba, are uniformly dispersed across the genome (Hofstatter et al. 2022). ...
Background and Aims
Genomic changes triggered by polyploidy, chromosomal rearrangements, and/ or environmental stress are among factors that affect the activity of mobile elements, particularly Long Terminal Repeats Retrotransposons (LTR-RTs) and DNA transposons. Because these elements can proliferate and move throughout host genomes, altering the genetic, epigenetic and nucleotypic landscape, they have been recognized as a relevant evolutionary force. Beaksedges (Rhynchospora) stand out for their wide cosmopolitan distribution, high diversity (~400 spp.) and holocentric chromosomes related to high karyotypic diversity and a centromere-specific satDNA Tyba. This makes the genus an interesting model to investigate the interactions between repetitive elements, phylogenetic relationships, and ecological variables.
Methods
Here, we used comparative phylogenetic methods to investigate the forces driving the evolution of the entire set of mobile elements (mobilome) in the holocentric genus Rhynchospora. We statistically tested the impact of phylogenetic relationships, abundance of holocentromeric satDNA Tyba, diversity of repeatome composition, ecological variables, and chromosome number in mobile element diversification.
Key Results
Tyba abundance was found to be inversely correlated with LTR-RT content. Decrease of LTR abundance and diversity was also related to increase in chromosome number (likely due to fission events), and colonization of dry environments in the northern hemisphere. In contrast, we found constant LTR insertions throughout time in species with lower chromosome numbers in rainier environments in South America. A multivariate model showed that different traits drive LTR abundance, especially repeat diversity and Tyba abundance. Other mobile elements, such as non-LTR RTs and DNA transposons had insufficient abundance to be included in our models.
Conclusions
Our findings suggest that LTR evolution is strongly impacted by the holocentric characteristics of Rhynchospora chromosomes, correlating with species diversification and biome shifts, and supporting a holokinetic drive model of evolution and a competitive scenario with Tyba. Altogether, our results present evidence of multi-trait influence on LTR-RT dynamics and provide a broader understanding of TE evolution in a macroevolutionary context.
... bustard, showed an almost total hybridisation of 17 BAC clones specific of GGA-1 (with the exception of the 5 th marker which not found on the CUN-1). Nevertheless, it was noted that 6 th marker is located on the short p arm of GGA-1 whereas it is found on the q arm of CUN-1 (Kiazim et al. 2021). According to the latest classification of birds, the orders of Colombiformes and Cuculiformes are very close to Otidiformes (Prum et al. 2015). ...
... A similar result was observed on chromosomes 1 of the Mallard Anas platyrhynchos and the Helmeted guineafowl Numida meleagris. In this study additional of evidence for centromere repositioning in birds was reported (Kiazim et al. 2021). The use of chromosome painting with chicken-specific probes in five Columbidae species showed significant conservation of chromosome 1 organisation, notably in Columbina talpacoti and Columbina passerina . ...
... While the hybridisation of specific probes of the GGA-7 on the metaphases of the Guinea fowl Numida meleagris revealed the presence of a pericentric inversion (Shibusawa et al. 2002). It would also seem to be the case of CUN-7 in which an inversion has been reported (Kiazim et al. 2021). Only molecular studies could elucidate such evolutionary events. ...
Birds are one of the most diverse groups among terrestrial vertebrates. They evolved from theropod dinosaurs, are closely related to the sauropsid group and separated from crocodiles about 240 million years ago. According to the IUCN, 12% of bird populations are threatened with potential extinction. Classical cytogenetics remains a powerful tool for comparing bird genomes and plays a crucial role in the preservation populations of endangered species. It thus makes it possible to detect chromosomal abnormalities responsible for early embryonic mortalities. Thus, in this work, we have provided new information on part of the evolutionary history by analysing high-resolution GTG-banded chromosomes to detect inter- and intrachromosomal rearrangements in six species. Indeed, the first eight autosomal pairs and the sex chromosomes of the domestic fowl Gallus gallus domesticus Linnaeus, 1758 were compared with five species, four of which represent the order Galliformes (Common and Japanese quail, Gambras and Chukar partridge) and one Otidiformes species (Houbara bustard).
Our findings suggest a high degree of conservation of the analysed ancestral chromosomes of the four Galliformes species, with the exception of (double, terminal, para and pericentric) inversions, deletion and the formation of neocentromeres (1, 2, 4, 7, 8, Z and W chromosomes). In addition to the detected rearrangements, reorganisation of the Houbara bustard chromosomes mainly included fusions and fissions involving both macro- and microchromosomes (especially on 2, 4 and Z chromosomes). We also found interchromosomal rearrangements involving shared microchromosomes (10, 11, 13, 14 and 19) between the two analysed avian orders. These rearrangements confirm that the structure of avian karyotypes will be more conserved at the interchromosomal but not at intrachromosomal scale.
The appearance ofa small number of inter- and intrachromosomal rearrangements that occurred during evolution suggests a high degree of conservatism of genome organisation in these six species studied. A summary diagram of the rearrangements detected in this study is proposed to explain the chronology of the appearance of various evolutionary events starting from the ancestral karyotype.
... In general, bird karyotypes have a low level of interchromosomal rearrangements (Griffin et al., 2008;Damas et al., 2018) and at the same time a high average rate of intrachromosomal rearrangements (Damas et al., 2019;O'Connor et al., 2024). Chicken BAC probes mapped onto Anas platy rhyn chos chromosomes have revealed the presence of inversions in all macrochromosomes and in the Z chromosome of the duck relative to the chicken (Fillon et al., 2007;Kiazim et al., 2021). However, conservation of gene order among several Anseriformes species has been detected by means of gene-specific probes (Islam et al., 2014). ...
... thesized that avian microchromosomes represent archaic linkage groups of ancestral vertebrates and have been preserved in a conserved state throughout the evolution of birds (Burt, 2002;Nakatani et al., 2007). Among Anatidae species, only A. platyrhynchos microchromosomes have been examined by FISH with chicken BAC probes, and the obtained data have confirmed the idea of high conservatism of avian genomes (Fillon et al., 2007;Kiazim et al., 2021). The set of BOE painting probes covered not all duck microchromosomes (see the Table, Fig. 3). ...
Galliformes and Anseriformes are two branches of the Galloanserae group, basal to other Neognathae. In contrast to Galliformes, Anseriformes have not been thoroughly researched by cytogenetic methods. This report is focused on representatives of Anseriformes and the evolution of their chromosome sets. Detailed cytogenetic analysis (G-banding, C-banding, and fluorescence in situ hybridization) was performed on three duck species: the northern pintail (Anas acuta, 2n = 80), the mallard (A. platyrhynchos, 2n = 80), and the common goldeneye (Bucephala clangula, 2n = 80). Using stone curlew (Burhinus oedicnemus, 2n = 42, Charadriiformes) chromosome painting probes, we created homology maps covering macrochromosomes and some microchromosomes. The results indicated a high level of syntenic group conservation among the duck genomes. The two Anas species share their macrochromosome number, whereas in B. clangula, this number is increased due to fissions of two ancestral elements. Additionally, in this species, the presence of massive heterochromatic blocks in most macroautosomes and sex chromosomes was discovered. Localization of clusters of ribosomal DNA and telomere repeats revealed that the duck karyotypes contain some microchromosomes that bear ribosomal RNA genes and/or are enriched for telomere repeats and constitutive heterochromatin. Dot plot (D-GENIES) analysis confirmed the established view about the high level of syntenic group conservation among Anatidae genomes. The new data about the three Anatidae species add knowledge about the transformation of macro- and sex chromosomes of Anseriformes during evolution.
... This approach offers higher resolution compared to traditional chromosome banding and chromosome painting techniques. In these studies, two or more BACs were chosen from each chicken chromosome that had been sequenced (from GGA1 to GGA28, excluding GGA16) to investigate interchromosomal rearrangements, or multiple BACs employed for intrachromosomal analyses [27,[39][40][41]. In the species examined, the microchromosomes homologous to chicken microchromosomes 22, 24, 26, and 27 consistently remain intact as whole segments, showing no evidence of chromosomal fusion. ...
... FISH hybridization of BAC probes allows for the identification of organizational and structural changes within avian genomes that can point the way for further whole genome sequencing studies to follow. While preceding comparable approaches in other vertebrate classes and further genome sequencing studies in birds and reptiles, the FISH and BAC-based investigative approaches and targeted aims offer to advance broadly the knowledge of comparative aspects of avian genome organization and implicate genomic changes in the evolutionary diversification and adaptive radiation of birds [27,41,[119][120][121]. Focusing, for example, on homologs to GGA3 and GGA4 provide particular insights into these processes. ...
In the last 100 years or so, much information has been accumulated on avian karyology, genetics, physiology, biochemistry and evolution. The chicken genome project generated genomic resources used in comparative studies, elucidating fundamental evolutionary processes, much of it funded by the economic importance of domestic fowl (which are also excellent model species in many areas). Studying karyotypes and whole genome sequences revealed population processes, evolutionary biology, and genome function, uncovering the role of repetitive sequences, transposable elements and gene family expansion. Knowledge of the function of many genes and non-expressed or identified regulatory components is however still lacking. Birds (Aves) are diverse and have striking adaptations for flight, migration and survival; they inhabit all continents and most islands. They also have a unique karyotype with ~ 10 macrochromosomes and ~ 30 microchromosomes that are smaller than other reptiles. Classified into Palaeognathae and Neognathae they are evolutionarily close, and a subset of reptiles. Here we overview avian molecular cytogenetics with reptilian comparisons, shedding light on their karyotypes and genome structure features. We consider avian evolution, then avian (followed by reptilian) karyotypes and genomic features. We consider synteny disruptions, centromere repositioning, and repetitive elements before turning to comparative avian and reptilian genomics. In this context, we review comparative cytogenetics and genome mapping in birds as well as Z- and W-chromosomes and sex determination. Finally, we give examples of pivotal research areas in avian and reptilian cytogenomics, particularly physical mapping and map integration of sex chromosomal genes, comparative genomics of chicken, turkey and zebra finch, California condor cytogenomics as well as some peculiar cytogenetic and evolutionary examples. We conclude that comparative molecular studies and improving resources continually contribute to new approaches in population biology, developmental biology, physiology, disease ecology, systematics, evolution and phylogenetic systematics orientation. This also produces genetic mapping information for chromosomes active in rearrangements during the course of evolution. Further insights into mutation, selection and adaptation of vertebrate genomes will benefit from these studies including physical and online resources for the further elaboration of comparative genomics approaches for many fundamental biological questions.
... In contrast to mammals, birds therefore exhibit a slow rate of change in interchromosomal rearrangements [65][66][67]. Despite this apparently slow rate, it is likely that the same does not apply to intrachromosomal rearrangements, which are seen considerably more frequently [68][69][70]. A comparison of the genomes of the chicken, turkey, and zebra finch and analysis using the Genalyzer tool [71] revealed a high degree of intrachromosomal rearrangement within the macrochromosomes, many of which were subsequently confirmed by FISH. ...
... Identification of the genomic features unique to these BACs using a bioinformatic approach [132,138] led to a refinement in the methods used to select BACs designed to hybridize across multiple species [8,70,114,132,139,140]. This resulted in an improvement in hybridization rates between species by several orders of magnitude. ...
... This resulted in an improvement in hybridization rates between species by several orders of magnitude. Selection of the BACs was based on successful hybridization across five core avian species [70,132] and by the position of each BAC in the reference species (at the most distal region of each chromosome). These BACs provided a consistent anchor point from which to compare species to track chromosomal rearrangements over time. ...
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.
... Aside from chromosomal rearrangements, centromeres are also suggested to contribute to broadscale F ST peaks in flycatchers [20]. Previous work has shown that centromere shifts occur in birds [65], which could also explain some of the changes in recombination rate between taiga flycatcher and collared flycatcher. Nevertheless, in several instances we find multiple F ST peaks per chromosome, a signature not expected if F ST peaks solely coincide with centromeres but pointing towards another mechanism, such as chromosomal rearrangements. ...
Recombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes, and consequently is expected to influence the efficacy of direct selection via Hill–Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, the impact of evolutionary changes in recombination rate on genomic signatures of selection remains largely unexplored. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (Ficedula albicilla) and collared flycatcher (Ficedula albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection, and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.
... 2. Кариотип домашних кур устроен сложно [32][33][34], о чем свидетельствует рисунок 2. ...
... Средний размер микрохромосом составляет 12,5 Мб, причем самый маленький из них равен 7 Мб. На микрохромосомы приходится 30% генома сельскохозяйственных кур [33]. ...
... They are extremely conservative in terms of chromosome number and content. Strong chromosomal synteny between different bird species and even between birds and reptiles indicates that interchromosomal rearrangements, such as translocations, were rarely fixed during their evolution, while intrachromosomal rearrangements, such as inversions and centromere shifts, were abundant [24][25][26][27][28]. Recently, metapolycentromeres have been described in several bird species [29]. ...
Simple Summary
Meiotic recombination, which involves the reshuffling of genes, plays an important role in generating biodiversity. However, studies on this process in bird chromosomes are scarce. Using antibodies targeting proteins involved in recombination, we examined the number of recombination events across the entire genome and their distribution along the largest chromosome in the germ cells of four closely related songbird species: Common linnet, Eurasian bullfinch, Eurasian siskin, and European goldfinch. We found significant variance in the frequency of recombination events among these species, as well as individual variability within each species. Across all four species, the distribution of recombination events on chromosome 1 was remarkably consistent, with more events occurring toward the chromosome ends and fewer near the centromere. The proximity of these events to the centromere depended on how many events took place on that chromosome, with more events being associated with closer locations. Interestingly, the size and type of the centromere did not influence this pattern. We propose that the scarcity of recombination events near the centromere may result from their sequential occurrence along the chromosome, starting from the chromosome ends, rather than from any specific influence from the centromere itself.
Abstract
Meiotic recombination is an important source of genetic diversity. Using immunolocalization of several meiotic proteins at the spreads of male pachytene cells, we estimated the number of recombination nodules per cell and their distribution along the macrochromosome 1 of the Common linnet, Eurasian bullfinch, Eurasian siskin, and European goldfinch. The macrochromosomes of the two former species have metapolycentromeres, composed of several centromeric domains. We detected significant interspecies differences in the mean numbers of recombination nodules per genome: 52.9 ± 2.8 in the linnet, 49.5 ± 3.5 in the bullfinch, 61.5 ± 6.3 in the siskin and 52.2 ± 2.7 in the goldfinch. Recombination patterns on macrochromosome 1 were similar across species, with more nodules localized near chromosome ends and fewer around centromeres. The distance from the proximal nodule to the centromere depended on the nodule count per chromosome arm, with more events leading to a closer location. However, species with different centromere types showed no difference in this regard. We propose that the deficiency of recombination sites near centromeres could be due to the sequential occurrence of crossovers starting from the chromosome ends and may not be attributed to any suppressive effect of the centromere itself.
... While interchromosomal rearrangements involving microchromosomes are relatively uncommon in birds, certain orders, such as Psittaciformes, Falconiformes, and Cuculiformes, have been found to exhibit this type of rearrangement more frequently than others [3,22]. However, despite detailed analysis of multiple bird orders, no interchromosomal rearrangements involving microchromosomes have been detected and shared among the analyzed orders, not even among closely related species [22,23]. These findings suggest that convergent evolution involving microchromosome rearrangements is an exceedingly rare occurrence in the class Aves. ...
... Our molecular cytogenetic characterization, which utilized BAC FISH microchromosomes probes from Chicken and Zebra Finch, demonstrated that all the microchromosomes tested in four Passeriformes species are conserved as complete units. This finding reinforces previous research indicating a high degree of conservation of microchromosomes in Passeriformes as well as in most avian species [23,28,36,37]. According to Burt [10], the distinct genomic characteristics exhibited by microchromosomes, including elevated GC content; reduced repeats; and increased gene density play a significant role in preserving these chromosomes as whole units in avian karyotypes. ...
... Thus, the absence of interchromosomal rearrangements observed in the majority of the analyzed Passeriformes species may be linked to the evolutionary success of this group, which represents one of the most diverse and highly derived clades within Aves [36,43]. 23,4,6 both the macrochromosomes and microchromosomes [37]. However, we cannot entirely rule out the possibility of microchromosome fusions occurring in the species investigated, as we were not able to analyze microchromosomes 16 and 29-38 due to a lack of probes for these chromosomes. ...
Passeriformes birds are widely recognized for their remarkable diversity, with over 5700 species described so far. Like most bird species, they possess a karyotype characteristic of modern birds, which includes a bimodal karyotype consisting of a few pairs of macrochromosomes and many pairs of microchromosomes. Although the karyotype is typically 2n = 80, the diploid number can atypically vary greatly, ranging from 56 to approximately 100 chromosomes. In this study, we aimed to understand the extent of conservation of the karyotype’s organizational structure within four species of this group using Bacterial Artificial Chromosomes via Fluorescence In Situ Hybridization (BAC-FISH) with microchromosome probes from Chicken (Gallus gallus) or Zebra Finch (Taeniopygia guttata) per microchromosomes (GGA10-28, except GGA16). By examining the chromosome complement of four passerine species—the Streaked Flycatcher (Myiodynastes maculatus), Shiny Cowbird (Molothrus bonariensis), Southern House Wren (Troglodytes aedon), and Double-collared Seedeater (Sporophila caerulescens)—we discovered a new chromosome number for Southern House Wren. Through FISH experiments, we were able to observe the same pattern of microchromosome organization as in the common ancestor of birds. As a result, we propose a new diploid number for Southern House Wren and confirm the conservation status of microchromosome organization, which may confer evolutionary advantages to this group.
... The web tool makes it possible to identify and characterize msHSBs, EBRs, their localization, including their start and end positions (in bp), and their length (Murphy et al. 2005;Romanov et al. 2014b). Evolution Highway was previously used for studying many avian species (e.g., Romanov et al. 2014b;Farré et al. 2016;O'Connor et al. 2018a,b;Kiazim et al. 2021). As aforementioned, we used the chicken genome as the reference, applied it to the total set of chromosomes available in the genomes of zebra finch, Pekin duck, turkey, budgerigar and ostrich, and aligned with them at the 300-Kb resolution. ...
Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.
