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Gene localization on California condor metaphase chromosomes following FISH using BAC clones labeled with biotin and counterstained with propidium iodide (a, b), or 2-color FISH using biotin- and digoxigenin-labeled clones withHoechst 33258 counterstaining (c, d). aSUPT3H and RUNX2 (clone 13G5) on chromosome 3q, bBTK (1N8) near the centromere of chromosome 9 with hybridization of an uncharacterized repeat to the W chromosome (green arrowhead), cOVM (5J24, biotin) and NR3C1 (29N19, digoxigenin) on chromosome 14, dUSP5 (1D23, biotin) and OCA2 (5D3, digoxigenin) on chromosome 1. In figures 1 and 2, biotin-FITC signals appear yellow or green, while digoxigenin-CY3 probes are red.
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Evolutionary cytogenetic comparisons involved 5 species of birds (California condor, chicken, zebra finch, collared flycatcher and black stork) belonging to divergent taxonomic orders. Seventy-four clones from a condor BAC library containing 80 genes were mapped to condor chromosomes using FISH, and 15 clones containing 16 genes were mapped to the...
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Citations
... The number of positive clones ranged between 1 to 15. For instance, in the California condor BAC library CHORI-262, we identified one positive clone CH262-037I12 that was putatively mapped in silico to the W chromosome and was further used for FISH on the Z and W in this endangered species and other birds Modi et al. 2009). ...
... In a previous study ), the California condor clone CHORI-262 37I12 positive for the chicken UBE2R2L overgo was cytogenetically mapped by FISH to the condor Z-linked homolog, with no signal being determined on the W chromosome. Similarly, use of the same condor W-linked clone on the black stork chromosomes revealed its localization on Zq near telomere (though the stork W was not looked at; Modi et al. 2009;Fig. 6). ...
Exploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative cytogenomic studies. Using bioinformatic, molecular (overgo BAC library scanning), and cytogenetic (BAC-based FISH) techniques, we have investigated in detail a pair of UBE2R2/UBE2R2L gametologs. By screening a gridded genomic jungle fowl BAC library, CHORI-261, with a short labeled UBE2R2L gene fragment called overgo probe, we detected seven specific clones. For three of them, CH261-019I23, CH261-105E16, and CH261-114G22, we identified their precise cytogenetic location on the Gallus gallus W chromosome (GGAW). They also co-localized with the UBAP2L2 gene on the, as was shown previously, along with the CH261-053P09 BAC clone also containing the GGAW-specific UBE2R2L DNA sequence. The fine mapping of the UBE2R2/UBE2R2L homologs in the chicken genome also shed the light on comparative cytogenetic aspects in birds. Our findings provided further evidence that bird genomes moderately changed only during evolution and are suitable for successful use of interspecies hybridization using both overgo-based BAC library screen and BAC-based FISH.
... With information about several species' CLAs at our disposal, comparative genomics is much more practical in silico [6]. While the auxiliary method of cross-species fluorescence in situ hybridization (zoo-FISH) can uncover further chromosome rearrangements that are difficult to detect using conventional karyotyping (e.g., [7][8][9][10]), comparative genomics enables us to outline the genome structure of less well-studied species (e.g., [8,11,12]) and reveal the chromosome rearrangements that led to each species' distinct karyotype (e.g., [10]) using a reference species as a benchmark, e.g., chickens. The relevance and genomic correlates of such chromosome constituents as evolutionary breakpoint regions (EBRs) and homologous synteny blocks (HSBs) that are features of chromosome evolution [6], as well as the mechanisms behind chromosomal breakage and fusion, can all be addressed with the use of CLAs. ...
... With information about several species' CLAs at our disposal, comparative genomics is much more practical in silico [6]. While the auxiliary method of cross-species fluorescence in situ hybridization (zoo-FISH) can uncover further chromosome rearrangements that are difficult to detect using conventional karyotyping (e.g., [7][8][9][10]), comparative genomics enables us to outline the genome structure of less well-studied species (e.g., [8,11,12]) and reveal the chromosome rearrangements that led to each species' distinct karyotype (e.g., [10]) using a reference species as a benchmark, e.g., chickens. The relevance and genomic correlates of such chromosome constituents as evolutionary breakpoint regions (EBRs) and homologous synteny blocks (HSBs) that are features of chromosome evolution [6], as well as the mechanisms behind chromosomal breakage and fusion, can all be addressed with the use of CLAs. ...
Simple Summary
Dinosaurs have been in scientific and popular culture since early fossil discoveries, but increased interest, particularly in their genomes, is expanding. Birds are reptiles, specifically theropod dinosaurs, meaning that if we compare the genomes of related reptile relations, we can get an idea of what the extinct dinosaur genomes looked like. In all animals/plants/fungi, we think of genome organization in terms of chromosomes. Genes sit on chromosomes and each cell of each individual of each species has its own unique organization. Every gene is in exactly the same spot on each chromosome, organized like continents and islands, with the genes as the cities/ towns/villages. All reptiles apart from crocodilians have both big and small chromosomes in their genomes but birds particularly so, like the Philippines or Polynesia. Birds have ~80 chromosomes (far more than most organisms) and this is very consistent in most species. Recent studies suggest that this pattern was probably established ~255 million years ago as it is also mostly present in some turtles. In other words, most dinosaurs probably had chromosomes (genome organization) like chickens or emus. In this paper, we present ideas of how this may have contributed to dinosaurs being so diverse in appearance and function.
Abstract
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome‐level genome assemblies cannot be made from long‐extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro‐ and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft‐shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine–Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
... With information about several species' CLAs at our disposal, comparative genomics is much more practical in silico [6]. While the auxiliary method of cross-species fluorescence in situ hybridization (zoo-FISH) can uncover further chromosome rearrangements that are difficult to detect using conventional karyotyping (e.g., [7][8][9][10]), comparative genomics enables us to outline the genome structure of less well-studied species (e.g., [8,11,12]) and reveal the chromosome rearrangements that led to each species' distinct karyotype (e.g., [10]) using a reference species as a benchmark, e.g., chickens. The relevance and genomic correlates of such chromosome constituents as evolutionary breakpoint regions (EBRs) and homologous synteny blocks (HSBs) that are features of chromosome evolution [6], as well as the mechanisms behind chromosomal breakage and fusion, can all be addressed with the use of CLAs. ...
... With information about several species' CLAs at our disposal, comparative genomics is much more practical in silico [6]. While the auxiliary method of cross-species fluorescence in situ hybridization (zoo-FISH) can uncover further chromosome rearrangements that are difficult to detect using conventional karyotyping (e.g., [7][8][9][10]), comparative genomics enables us to outline the genome structure of less well-studied species (e.g., [8,11,12]) and reveal the chromosome rearrangements that led to each species' distinct karyotype (e.g., [10]) using a reference species as a benchmark, e.g., chickens. The relevance and genomic correlates of such chromosome constituents as evolutionary breakpoint regions (EBRs) and homologous synteny blocks (HSBs) that are features of chromosome evolution [6], as well as the mechanisms behind chromosomal breakage and fusion, can all be addressed with the use of CLAs. ...
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine–Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
... By the end of 2019, the extant population consisted of 525 birds, 219 in captivity and 306 wild individuals free-flying in California, Arizona, Utah (including the Grand Canyon area and Zion National Park), and Baja California (Mace 2019). The successful restoration program also benefited from genetic and genomic research projects in this endangered species (Romanov et al. 2006;Modi et al. 2009). A California condor microsatellite-enriched library and a set of polymorphic microsatellite markers were generated and used as an instrument for genetic studies ). ...
Parthenogenesis is a relatively rare event in birds, documented in unfertilized eggs from columbid, galliform, and passerine females with no access to males. In the critically endangered California condor, parentage analysis conducted utilizing polymorphic microsatellite loci has identified two instances of parthenogenetic development from the eggs of two females in the captive breeding program, each continuously housed with a reproductively capable male with whom they had produced offspring. Paternal genetic contribution to the two chicks was excluded. Both parthenotes possessed the expected male ZZ sex chromosomes and were homozygous for all evaluated markers inherited from their dams. These findings represent the first molecular marker-based identification of facultative parthenogenesis in an avian species, notably of females in regular contact with fertile males, and add to the phylogenetic breadth of vertebrate taxa documented to have reproduced via asexual reproduction. (CORRECTED PROOF)
... Степень эволюционной дивергенции между геномами близких и удаленных видов птиц можно также оценивать посредством ДНК-гибридизации с применением overgo-проб [26,35,36,[38][39][40]. ...
This review highlights the main issues related to the cytogenomics of birds (class Aves), including the special organization and evolution of their genome and chromosomes.
Key words: birds, Aves, cytogenomics, genome organization, chromosomes, evolution
В обзоре освещены основные вопросы, касающиеся цитогеномики птиц (класс Aves), включая особую организацию и эволюцию их генома и хромосом.
Ключевые слова: птицы, Aves, цитогеномика, организация генома, хромосомы, эволюция
... Selection can occur during extended in vitro culturing; for example, while subculturing California condor feather pulp-derived fibroblasts, an apparent mutation resulting in spontaneous overexpression of mRNA for the mitotic arrest deficient-like 1 protein occurred, which in this case was useful for repeated harvesting of metaphase chromosome (5,6). ...
Because living cells can be saved for indefinite periods, unprecedented opportunities for characterizing, cataloging, and conserving biological diversity have emerged as advanced cellular and genetic technologies portend new options for preventing species extinction. Crucial to realizing the potential impacts of stem cells and assisted reproductive technologies on biodiversity conservation is the cryobanking of viable cell cultures from diverse species, especially those identified as vulnerable to extinction in the near future. The advent of in vitro cell culture and cryobanking is reviewed here in the context of biodiversity collections of viable cell cultures that represent the progress and limitations of current efforts. The prospects for incorporating collections of frozen viable cell cultures into efforts to characterize the genetic changes that have produced the diversity of species on Earth and contribute to new initiatives in conservation argue strongly for a global network of facilities for establishing and cryobanking collections of viable cells.
... Compared to chicken, the only interchromosomal rearrangement identified was the ancestral 21 configuration of GGA4 found as two separate chromosomes in pigeon and other birds 22 (Derjusheva et al. 2004;Hansmann et al. 2009;Modi et al. 2009 Table S8). demo.ncsa.uiuc.edu/birds). ...
Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes. Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome level comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food and/or environmental reasons. Pigeon has a typical avian karyotype (2n=80) while falcon (2n=50) is highly rearranged compared to the avian ancestor. Using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved non-coding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE 'deserts.' This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
... Comparative screening of BAC libraries and FISH using BAC clones have also assisted in developing genomic resources and tools for the endangered California condor and the white-throated sparrow, a model for behavioral studies in humans [Romanov et al., , 2009a[Romanov et al., , b, 2011Thomas et al., 2008;Modi et al., 2009]. Kothapalli et al. [2011] examined California condor BACs harboring the immunoglobulin lambda locus and found a region of high homology to the chicken and zebra finch orthologs. ...
High-density gridded libraries of large-insert clones using bacterial artificial chromosome (BAC) and other vectors are essential tools for genetic and genomic research in chicken and other avian species...
Taken together, these studies demonstrate that applications of large-insert clones and BAC libraries derived from birds are, and will continue to be, effective tools to aid high-throughput and state-of-the-art genomic efforts and the important biological insight that arises from them.
... Delineating the process of sex chromosome differentiation is difficult in neognathous birds because of their extensively heteromorphic sex chromosomes. The order of Z-linked genes also differs between species as a result of independent intra-chromosomal rearrangements in each lineage [International Chicken Genome Sequencing Consortium, 2004;Backström et al., 2006;Itoh et al., 2006;Modi et al., 2009]. By contrast, sex chromosome differentiation was slower in ratites than in neognathous birds. ...
The W chromosome of ratite birds shows minimal morphological differentiation and retains homology of genetic linkage and gene order with a substantial stretch of the Z chromosome; however, the molecular structure in the differentiated region is still not well known. The kW1 sequence was isolated from the kiwi as a W-specific DNA marker for PCR-based molecular sexing of ratite birds. In ratite W chromosomes, this sequence commonly contains a ∼200-bp deletion. To characterize the very early event of avian sex chromosome differentiation, we performed molecular cytogenetic analyses of kW1 and its flanking sequences in paleognathous and neognathous birds and reptiles. Female-specific repeats were found in the kW1-flanking sequence of the cassowary (Casuarius casuarius), and the repeats have been amplified in the pericentromeric region of the W chromosomes of ratites, which may have resulted from the cessation of meiotic recombination between the Z and W chromosomes at an early stage of sex chromosome differentiation. The presence of the kW1 sequence in neognathous birds and a crocodilian species suggests that the kW1 sequence was present in the ancestral genome of Archosauria; however, it disappeared in other reptilian taxa and several lineages of neognathous birds. © 2014 S. Karger AG, Basel.
... Furthermore, comparative chromosome mapping has enabled us to identify intrachromosomal rearrangements, which cannot be detected precisely by chromosome painting. However, comparative chromosome mapping with functional genes and/or cytogenetic DNA markers has been performed for a few avian species (including the California condor, domestic duck, flycatchers, Guinea fowl, Japanese quail, New World quails, turkey, and zebra finch) (Shibusawa et al., 2001(Shibusawa et al., , 2002(Shibusawa et al., , 2004aItoh et al., 2006;Fillon et al., 2007;Stapley et al., 2008;Modi et al., 2009;Skinner et al., 2009;Backström et al., 2010;Zhang et al., 2011). Therefore, a lack of information of intrachromosomal rearrangements between dif-ferent species makes it difficult to delineate the process of avian karyotype evolution precisely. ...
To better understand the process of karyotype evolution in Galloanserae (Galliformes and Anseriformes), we performed comparative chromosome painting with chicken chromosome-specific DNA probes and FISH mapping of the 18S-28S ribosomal RNA (rRNA) genes, telomeric (TTAGGG)n repeats, and cDNA clones of 37 genes for three anserid species, the domestic duck (Anas platyrhynchos), Muscovy duck (Cairina moschata), and Chinese goose (Anser cygnoides). Each chicken probe of chromosomes 1-9 and the Z chromosome painted a single pair of chromosomes in the three species except for the chromosome 4 probe, which painted acrocentric chromosome 4 and a pair of microchromosomes. The 18S-28S rRNA genes were localized to four pairs of microchromosomes in the domestic duck and Muscovy duck, and eight pairs of microchromosomes in the Chinese goose. The (TTAGGG)n repeats were localized to both telomeric ends of all chromosomes in the three species, and were additionally located in the interstitial region of the short arm of chromosome 1 in the domestic duck and in the centromeric region of chromosome 1 in the Muscovy duck. Comparative gene mapping of 37 chicken chromosome 1-4-linked and Z-linked genes revealed high chromosome homologies among three anserid species and also between the chicken and the three anserid species, although there were several chromosome rearrangements: pericentric inversion in chromosome 2, pericentric and paracentric inversions or centromere repositioning in the Z chromosome between the chicken and the anserid species, and pericentric inversions in chromosome 4 and the Z chromosome between the Chinese goose and the two duck species. These results collectively suggest that karyotypes have been highly conserved in Anseriformes and that chromosome rearrangements also occurred less frequently between Galliformes and Anseriformes after they diverged around 100 million years ago.
