Origin and evolution of avian microchromosomes

The origin of avian microchromosomes has long been the subject of much speculation and debate. Microchromosomes are a universal characteristic of all avian species and many reptilian karyotypes. The typical avian karyotype contains about 40 pairs of chromosomes and usually 30 pairs of small to tiny microchromosomes. This characteristic karyotype probably evolved 100-250 million years ago. Once the microchromosomes were thought to be a non-essential component of the avian genome. Recent work has shown that even though these chromosomes represent only 25% of the genome; they encode 50% of the genes. Contrary to popular belief, microchromosomes are present in a wide range of vertebrate classes, spanning 400-450 million years of evolutionary history. In this paper, comparative gene mapping between the genomes of chicken, human, mouse and zebrafish, has been used to investigate the origin and evolution of avian microchromosomes during this period. This analysis reveals evidence for four ancient syntenies conserved in fish, birds and mammals for over 400 million years. More than half, if not all, microchromosomes may represent ancestral syntenies and at least ten avian microchromosomes are the product of chromosome fission. Birds have one of the smallest genomes of any terrestrial vertebrate. This is likely to be the product of an evolutionary process that minimizes the DNA content (mostly through the number of repeats) and maximizes the recombination rate of microchromosomes. Through this process the properties (GC content, DNA and repeat content, gene density and recombination rate) of microchromosomes and macrochromosomes have diverged to create distinct chromosome types. An ancestral genome for birds likely had a small genome, low in repeats and a karyotype with microchromosomes. A "Fission-Fusion Model" of microchromosome evolution based on chromosome rearrangement and minimization of repeat content is discussed.     

FISH mapping of 57 BAC clones reveals strong conservation of synteny between Galliformes and Anseriformes

Karyotypes of chicken (Gallus gallus domesticus; 2n = 78) and mallard duck (Anas platyrhynchos; 2n = 80) share the typical organization of avian karyotypes including a few macrochromosome pairs, numerous indistinguishable microchromosomes, and Z and W sex chromosomes. Previous banding studies revealed great similarities between chickens and ducks, but it was not possible to use comparative banding for the microchromosomes. In order to establish precise chromosome correspondences between these two species, particularly for microchromosomes, we hybridized 57 BAC clones previously assigned to the chicken genome to duck metaphase spreads. Although most of the clones showed similar localizations, we found a few intrachromosomal rearrangements of the macrochromosomes and an additional microchromosome pair in ducks. BAC clones specific for chicken microchromosomes were localized to separate duck microchromosomes and clones mapping to the same chicken microchromosome hybridized to the same duck microchromosome, demonstrating a high conservation of synteny. These results demonstrate that the evolution of karyotypes in avian species is the result of fusion and/or fission processes and not translocations.     

Molecular cytogenetic study on the ploidy status in Acipenser mikadoi

The ploidy status of Acipenser mikadoi was examined using nuclear DNA contents, karyotypes and fluorescence in situ hybridization (FISH) with 5.8S + 28S rDNA as a probe. In flow‐cytometrically sorted specimens with 8.2–9.1 pg DNA content per somatic cell, i.e. genetic diploid, the best informative metaphase with 268 chromosomes had 80 biarmed meta‐ or submetacentric (M or SM) chromosomes, 48 monoarmed telocentric (T) chromosomes and 140 microchromosomes. In genetic triploid specimens with 12.6–13.0 pg DNA content, the best informative metaphase with 402 chromosomes showed 120 biarmed M or SM, 72 monoarmed T chromosomes and 210 microchromosomes. The rDNA FISH detected a maximum 18 and 27 signals in the diploid and triploid A. miakdoi, respectively. The obtained findings thus corroborated a clear parallel between nuclear DNA contents and karyological or FISH profiles in the genetic diploid and triploid specimens, suggesting 1.5 times chromosome complements of diploid counterparts or three sets of homologues in the triploid sturgeons. Moreover, the estimated genome size and the observed molecular cytogenetic features in the diploid A. mikadoi strongly suggest that this species is a member of a functional tetraploid group recently proposed in the literature.     

Selachian cytogenetics: a review

The karyotype of Chondrichthyes is still the least investigated among vertebrates. Over the last 40 years, the karyotypes of 63 out of the 1100 known species (5.73%) have been described in literature, namely seven squalomorph, one squatinomorph, 20 galeomorph, 33 batoid and two holocephalian species. Generally, the diploid number ranges from a minimum of 28 to a maximum of 106 elements, with more frequent values observed between 50 and 100 chromosomes. None of the four superorders is characterized by a peculiar chromosome set or morphology; the number of uniarmed and biarmed elements is variable in all the karyotypes, and microchromosomes are often present. The general trend in all groups seems to be a progressive reduction of the telocentric chromosome number in the most specialized species, followed by the loss of the microchromosomes. Polyploidy, followed by diploidization events and Robertsonian rearrangements, might have played a key role in the karyological evolution of elasmobranch fish. Chondrichthyes have the largest genome sizes among vertebrates, with the exception of dipnoans and urodeles. In the whole class, the species examined vary greatly in size, from 3 to 34pg/N: the lowest values have been observed in holocephalians, while galeoids and batoids have a DNA amount ranging from 5 to 15 pg/N. Squaloids show heterogeneous DNA amounts, ranging from 8 to 34 pg/N. In more recent years, karyological studies have provided new data on the characterization of selachian karyotypes by C-banding, NOR staining, restriction enzymes in situ digestion and FISH with specific DNA probes, such as telomeric and SINE sequences.     

Karyotype study of 5 species of Costa Rican snakes of the colubrid family

The karyotypes of five species of colubrid snakes from Costa Rica are as follows: Imantodes cenchoa and Drymobius margaritiferus have a diploid number of 36, with 16 macro- and 20 microchromosomes. The fourth pair is heteromorphic in females of I. cenchoa, with a metacentric Z and a submetacentric W chromosomes. Karyotypes of Erythrolampius bizonus and Leimadophis epinephalus have 28 chromosomes, without a clearcut separation between macro- and microchromosomes. In the case of E. bizomus, the fourth pair contains the sex chromosomes Z and W, both are submetacentric, but the W is smaller. Xenedon rabdocephalus has a diploid number of 34 chromosomes (22 macro- and 12 microchromosomes); pair 3 is heteromorphic in females, with a submetacentric Z and a smaller metacentric W. The karyotype of X. rabdocephalus may be derived from a primitive karyotype by means of reduction in the number of microchromosomes and centric fissions of two pairs of metacentric autosomes.     

Karyotypes, C-banding, and chromosomal location of active nucleolar organizing regions in Tapinoma (Hymenoptera, Formicidae)

The haploid and diploid karyotypes of Tapinoma erraticum (n = 8) and Tapinoma nigerrimum (n = 9) were analyzed using C-banding and observation of NOR sites. C-banding showed the existence of heterochromatin in the paracentromeric regions of all chromosomes. The analysis of NOR sites in these species proved the existence of primary activity NOR in one or two chromosomes, respectively, whereas the other chromosomes showed secondary activity NOR, expressed only in a minority of cells. In both species the NOR were located in paracentromeric regions. These results are discussed in relation to a hypothesis of chromosome differentiation of these species.     

The somatic chromosome complements of 16 species of falconiformes (Aves) and the karyological relationships of the order

Using short term leucocyte culture techniques, the somatic chromosome complements of 16 species of diurnal birds of prey, belonging to four different families of the order Falconiformes were studied. The karyotypes are described and illustrated, and of some species idiograms are presented. In accordance with the family classification, four karyologically different groups can be distinguished in the Falconiformes: (1) Cathartidae, with karyotypes which show only 7 pairs of biarmed macrochromosomes and a considerable number of small acrocentrics and microchromosomes (the diploid numbers are approximately 80). This is the only group in which really large macrochromosomes are found (over 10% TCL); (2) Falconidae, the karyotypes of which include only a single pair of biarmed macrochromosomes, all other elements being acrocentrics of medium to small size or microchromosomes (diploid numbers of approximately 84 and 52); (3) the secretary bird (Sagittariidae), with 36 biarmed macrochromosomes and 44 small acrocentrics and microchromosomes (2n=80 approximately); (4) Accipitridae, the representatives of which never possess more than about 8 real microchromosomes, while their karyotypes show varying numbers of biarmed and acrocentric macrochromosomes of small to medium size (diploid numbers range from 78 to 60).The possible karyological relationships within each of these groups are briefly discussed, while a more extensive discussion is dedicated to the possible relationships between these groups, and those between them and other avian taxa.The variation in karyotypic structures found in the Falconiformes is much wider than that in other avian groups. However, it remains an unanswered question whether this karyological heterogenelty points to a polyphyletic origin of the diurnal birds of prey. Especially the chromosome complements of the Accipitridae are most uncommon among birds, because of their extremely low numbers of real microchromosomes. However, of all the Falconiformes only the karyotypes of the Cathartidae have clear counterparts outside the order, since nearly identical complements were found in representatives of the Phoenicopteriformes and Gruiformes.The present work was partially carried out at the Institute of Genetics and the Center for Clinical Cytogenetics (both in Utrecht).     

Comparative study of genomes of two species of flax by C-banding of chromosomes

C-banding patterns of the karyotypes of two closely related wild flax species, Linum austriacum L. (2n = 18) and Linum grandiflorum Desf. (2n = 16), were studied. The karyotypes of both species were similar in the chromosome morphology and size. In each species, metacentric and acrocentric chromosomes (1.7-4.3 microns) and one satellite chromosome were observed. In the karyotypes of the species studied, all homologous chromosome pairs were identified, and quantitative ideograms were constructed. Eight chromosome pairs in the two species had similar C-banding patterns. A low level of intraspecific polymorphism in the intercalary and telomeric C-bands was shown in both species. The results indicate that the genomes of two flax species originated from one ancestral genome with the main chromosome number of 8 or 9. Apparently, the doubling of chromosome number or loss of one chromosome with subsequent redistribution of the chromosome material in the ancestral form resulted in the divergence into two species, L. austriacum L. and L. grandiflorum Desf. A considerable similarity of chromosomes in these species provides evidence for their close phylogenetic relatedness, which makes it possible to place them in one section within the Linum genus.     

Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes: Accipitridae)

The karyotypes of most birds consist of a small number of macrochromosomes and numerous microchromosomes. Intriguingly, most accipitrids which include hawks, eagles, kites, and Old World vultures (Falconiformes) show a sharp contrast to this basic avian karyotype. They exhibit strikingly few microchromosomes and appear to have been drastically restructured during evolution. Chromosome paints specific to the chicken (GGA) macrochromosomes 1-10 were hybridized to metaphase spreads of three species of Old World vultures (Gyps rueppelli, Gyps fulvus, Gypaetus barbatus). Paints of GGA chromosomes 6-10 hybridize only to single chromosomes or large chromosome segments, illustrating the existence of high chromosome homology. In contrast, paints of the large macrochromosomes 1-5 show split hybridization signals on the chromosomes of the accipitrids, disclosing excessive chromosome rearrangements which is in clear contrast to the high degree of chromosome conservation substantiated from comparative chromosome painting in other birds. Furthermore, the GGA chromosome paint hybridization patterns reveal remarkable interchromosomal conservation among the two species of the genus Gyps.     

Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences

The phylogenetic relationships of nine species of freshwater sponges, representing the families Spongillidae, Lubomirskiidae, and Metaniidae, were inferred from analyses of 18S rDNA, cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacer 2 (ITS2) rDNA sequences. These species form a strongly supported monophyletic group within the Demospongiae, with the lithistid Vetulina stalactites as the sister taxon. Within the freshwater sponge clade, the basal taxon is not resolved. Depending upon the method of analysis and sequence, the metaniid species, Corvomeyenia sp., or the spongillid species, Trochospongilla pennsylvanica , emerges as the basal species. Among the remaining freshwater sponge species, the spongillids, Spongilla lacustris and Eunapius fragilis , form a sister group to a clade comprised of the spongillid species, Clypeatula cooperensis , Ephydatia fluviatilis , and Ephydatia muelleri , and the lubomirskiid species, Baikalospongia bacillifera and Lubomisrkia baicalensis . C. cooperensis is the sister taxon of E. fluvialitis , and E. muelleri is the sister taxon of ( B. bacillifera + L. baicalensis ). The family Spongillidae and the genus Ephydatia are thus paraphyletic with respect to the lubomirskiid species; Ephydatia is also paraphyletic to C. cooperensis . We suggest that C. cooperensis be transferred to the genus Ephydatia and that the family Lubomirskiidae be subsumed into the Spongillidae.     

Comparative chromosome painting of chicken autosomal paints 1-9 in nine different bird species

In a Zoo-FISH study chicken autosomal chromosome paints 1 to 9 (GGA1-GGA9) were hybridized to metaphase spreads of nine diverse birds belonging to primitive and modern orders. This comparative approach allows tracing of chromosomal rearrangements that occurred during bird evolution. Striking homologies in the chromosomes of the different species were noted, indicating a high degree of evolutionary conservation in avian karyotypes. In two species, the quail and the goose, all chicken paints specifically labeled their corresponding chromosomes. In three pheasant species as well as in the American rhea and blackbird, GGA4 hybridized to chromosome 4 and additionally to a single pair of microchromosomes. Furthermore, in the pheasants fission of the ancestral galliform chromosome 2 could be documented. Hybridization of various chicken probes to two different chromosomes or to only the short or long chromosome arm of one chromosome pair in the species representing the orders Passeriformes, Strigiformes, and Columbiformes revealed translocations and chromosome fissions during species radiation. Thus comparative analysis with chicken chromosome-specific painting probes proves to be a rapid and comprehensive approach to elucidate the chromosomal relationships of the extant birds.     

Comparative Compositional Mapping of Chicken and Quail Chromosomes

The distribution of various isochore families on mitotic chromosomes of domestic chicken and Japanese quail was studied by the method of fluorescence in situ DNA–DNA hybridization (FISH). DNA of various isochore families was shown to be distributed irregularly and similarly on chromosomes of domestic chicken and Japanese quail. The GC-rich isochore families (H2, H3, and H4) hybridized mainly to microchromosomes and a majority of macrochromosome telomeric regions. In chicken, an intense fluorescence was also in a structural heterochromatin region of the Z chromosome long arm. In some regions of the quail macrochromosome arms, hybridization was also with isochore families H3 and H4. On macrochromosomes of both species, the pattern of hybridization with isochores of the H2 and H3 families resembled R-banding. The light isochores (L1 and L2 families) are mostly detected within macrochromosome internal regions corresponding to G bands, whereas microchromosomes lack light isochores. Although mammalian and avian karyotypes differ significantly in organization, the isochore distribution in genomes of these two lineages of the warm-blooded animals is similar in principle. On macrochromosomes of the two avian species studied, a pattern of isochore distribution resembled that of mammalian chromosomes. The main specific feature of the avian genome, a great number of microchromosomes (about 30% of the genome), determines a compositional specialization of the latter. This suggests the existence of not only structural but also functional compartmentalization of the avian genome.     

Cross-species chromosome painting in the Perissodactyla: delimitation of homologous regions in Burchell's zebra (Equus Burchellii) and the white (Ceratotherium Simum) and black rhinoceros (Diceros Bicornis)

Conserved chromosomal segments in the black rhinoceros, Diceros Bicornis (DBI, 2n = 84), and its African sister-species the white rhinoceros, Ceratotherium Simum (CSI, 2n = 82), were detected using Burchell's zebra (Equus Burchellii, EBU, 2n = 44) chromosome-specific painting probes supplemented by a subset of those developed for the horse (Equus Caballus, ECA, 2n = 64). In total 41 and 42 conserved autosomal segments were identified in C. Simum and D. Bicornis respectively. Only 21 rearrangements (20 fissions and 1 fusion) are necessary to convert the Burchell's zebra karyotype into that of the white rhinoceros. One fission distinguishes the D. Bicornis and C. Simum karyotypes which, excluding heterochromatic differences, are identical in all respects at this level of resolution. Most Burchell's zebra chromosomes correspond to two rhinoceros chromosomes although in four instances (EBU18, 19, 20 and 21) whole chromosome synteny has been retained among these species. In contrast, one rhinoceros chromosome (DBI1, CSI1) comprises two separate Burchell's zebra chromosomes (EBU11 and EBU17). In spite of the high diploid numbers of the two rhinoceros species their karyotypes are surprisingly conserved offering a glimpse of the putative ancestral perissodactyl condition and a broader understanding of genome organization in mammals.     

Chromosome banding in three species of <Emphasis Type="Italic">Hypsiboas</Emphasis> (Hylidae,Hylinae), with special reference to a new case of B-chromosome in anuran frogs and to the reduction of the diploid number of 2n = 24 to 2n = 22 in the genus

The chromosomes of hylids Hypsiboas albopunctatus, H. raniceps, and H. crepitans from Brazil were analyzed with standard and differential staining techniques. The former species presented 2n = 22 and 2n = 23 karyotypes, the odd diploid number is due to the presence of an extra element interpreted as B chromosome. Although morphologically very similar to the small-sized chromosomes of the A complement, the B was promptly recognized, even under standard staining, on the basis of some characteristics that are usually attributed to this particular class of chromosomes. The two other species have 2n = 24, which is the chromosome number usually found in the species of Hypsiboas karyotyped so far. This means that 2n = 22 is a deviant diploid number, resulted from a structural rearrangement, altering the chromosome number of 2n = 24 to 2n = 22. Based on new chromosome data, some possibilities were evaluated for the origin of B chromosome in Hypsiboas albopunctatus, as well as the karyotypic evolution in the genus, leading to the reduction in the diploid number of 2n = 24 to 2n = 22.     

Comparative analysis of diploid species of Avena l. using cytogenetic and biochemical markers: Avena canariensis baum et fedak and A. longiglumis dur

The diploid oat species containing the A genome of two types (Al and Ac) were studied by electrophoresis of grain storage proteins (avenins), chromosome C-banding, and in situ hybridization with probes pTa71 and pTa794. The karyotypes of the studied species displayed similar C-banding patterns but differed in size and morphology of several chromosomes, presumably, resulting from structural rearrangements that took place during the divergence of A genomes from a common ancestor. In situ hybridization demonstrated an identical location of the 45S and 5S rRNA gene loci in Avena canariensis and A. longiglumis similar to that in the A. strigosa genome. However, the 5S rDNA locus in A. longiglumis (5S rDNA1) was considerably decreased in the chromosome 3A1 long arm. The analysis demonstrated that these oat species were similar in the avenin component composition, although individual accessions differed in the electrophoretic mobilities of certain components. A considerable similarity of A. canariensis and A. longiglumis to the Avena diploid species carrying the As genome variant was demonstrated.     

Reversal and convergence in marsupial chromosome evolution

The karyotypes of marsupial species are characterized by their relatively low number of chromosomes, and their conservation. Most species have diploid numbers lying between the two modes, 2n = 14 and 2n = 22, but the karyotype of Aepyprymnus rufescens is exceptional in containing 2n = 32 chromosomes. Many differences in diploid number between marsupial species can be accounted for by particular fissions and fusions, which are easy to detect because of the low numbers of chromosomes in each karyotype. This should be a system in which it is possible to detect reversals and repeated chromosome rearrangements. We have used chromosome-specific paints derived from A. RUFESCENS to compare the karyotypes of eight marsupial species, representing closely and distantly related taxa, to trace chromosome change during evolution, and especially to detect reversals and convergence. From these and other painting comparisons, we conclude that there have been at least three reversals of fusions by fissions, and at least three fusions or fissions that have occurred independently in different lineages.     

Karyological study of Amphisbaena ridleyi (Squamata, Amphisbaenidae), an endemic species of the Archipelago of Fernando de Noronha, Pernambuco, Brazil

The karyotype of Amphisbaena ridleyi, an endemic species of the archipelago of Fernando de Noronha, in State of Pernambuco, Brazil, is described after conventional staining, Ag-NOR impregnation and fluorescence in situ hybridization (FISH) with a telomeric probe. The diploid number is 46, with nine pairs of macrochromosomes (three metacentrics, four subtelocentrics and two acrocentrics) and 14 pairs of microchromosomes. The Ag-NOR is located in the telomeric region of the long arm of metacentric chromosome 2 and FISH revealed signals only in the telomeric region of all chromosomes. Further cytogenetic data on other amphisbaenians as well as a robust phylogenetic hypothesis of this clade is needed in order to understand the evolutionary changes on amphisbaenian karyotypes.     

Identification of the sex chromosomes in the bald eagle.

Karyotypes of five American bald eagles (Haliaeetus leucocephalus and H. alacanus) are compared. All had 2n=66 chromosomes which fell into 3 size groups: A, 20 pairs of biarmed chromosomes; B, 9 pairs of acrocentric chromosomes and C, 4 pairs of microchromosomes. C-banding was done in two eagles and a heterochromatic W chromosome was identified in a presumptive female. The ZZ and ZW chromosomes could be identified in the karyotypes.     

New insights into sex chromosome evolution in anole lizards (Reptilia,Dactyloidae)

Anoles are a clade of iguanian lizards that underwent an extensive radiation between 125 and 65 million years ago. Their karyotypes show wide variation in diploid number spanning from 26 (Anolis evermanni) to 44 (A. insolitus). This chromosomal variation involves their sex chromosomes, ranging from simple systems (XX/XY), with heterochromosomes represented by either micro- or macrochromosomes, to multiple systems (X₁X₁X₂X₂/X₁X₂Y). Here, for the first time, the homology relationships of sex chromosomes have been investigated in nine anole lizards at the whole chromosome level. Cross-species chromosome painting using sex chromosome paints from A. carolinensis, Ctenonotus pogus and Norops sagrei and gene mapping of X-linked genes demonstrated that the anole ancestral sex chromosome system constituted by microchromosomes is retained in all the species with the ancestral karyotype (2n?=?36, 12 macro- and 24 microchromosomes). On the contrary, species with a derived karyotype, namely those belonging to genera Ctenonotus and Norops, show a series of rearrangements (fusions/fissions) involving autosomes/microchromosomes that led to the formation of their current sex chromosome systems. These results demonstrate that different autosomes were involved in translocations with sex chromosomes in closely related lineages of anole lizards and that several sequential microautosome/sex chromosome fusions lead to a remarkable increase in size of Norops sagrei sex chromosomes.