67 research outputs found
Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification
To investigate the distribution of LINE-1 repeat sequences, a
LINE-1 probe was Fluorescence In Situ Hybridized (FISH) on the
chromosomes of Ateles geoffroyi and Ateles fusciceps (Atelidae); a
LINE-1 probe was also mapped on Cebuella pygmaea (Cebidae)
and used as an outgroup for phylogenetic comparison. Ateles spider
monkeys have a highly rearranged genome and are an ideal model
for testing whether LINE-1 is involved in genome evolution. The
LINE-1 probe has been mapped in the two Atelidae species for the
first time, revealing a high accumulation of LINE-1 sequences
along chromosomal arms, including telomeres, and a scarcity of
LINE-1 signals at centromere positions. LINE-1 mapping in C. pygmaea (Cebidae) revealed signals at centromere positions and along
chromosome arms, which was consistent with previous published
data from other Cebidae species. In a broader sense, the results were
analyzed in light of published data on whole-chromosomal human
probes mapped in these genomes. This analysis allows us to speculate about the presence of LINE-1 sequences at the junction of
human chromosomal syntenies, as well as a possible link between
these sequences and chromosomal rearrangements
Repetitive sequence distribution on Saguinus, Leontocebus and Leontopithecus tamarins (Platyrrhine, Primates) by mapping telomeric (TTAGGG) motifs and rDNA loci
Tamarins are a distinct group of small sized New World monkeys with complex phylogenetic re-lationships and poorly studied cytogenetic traits. In this study, we applied molecular cytogenetic analyses by fluorescence in situ hybridization with probes specific for telomeric sequences and ri-bosomal DNA loci after DAPI/CMA3 staining on metaphases from five tamarin species, namely Leontocebus fuscicollis, Leontopithecus rosalia, Saguinus geoffroyi, Saguinus mystax and Saguinus oedi-pus, with the aim to investigate the distribution of repetitive sequences and their possible role in genome evolution. Our analyses revealed that all five examined species show similar karyotypes, 2n = 46, which differ mainly in the morphology of chromosome pairs 16–17 and 19–22, due to the diverse distribution of rDNA loci, the amplification of telomeric-like sequences, the presence of heterochromatic blocks and/or putative chromosomal rearrangements, such as inversions. The differences in cytogenetic traits between species of tamarins are discussed in a comparative phy-logenetic framework, and in addition to data from previous studies, we underline synapo-morphies and apomorphisms that appeared during the diversification of this group of New World monkeys
Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus)
BACKGROUND: Most eukaryotic species represent stable karyotypes with a particular diploid number. B chromosomes are additional to standard karyotypes and may vary in size, number and morphology even between cells of the same individual. For many years it was generally believed that B chromosomes found in some plant, animal and fungi species lacked active genes. Recently, molecular cytogenetic studies showed the presence of additional copies of protein-coding genes on B chromosomes. However, the transcriptional activity of these genes remained elusive. We studied karyotypes of the Siberian roe deer (Capreolus pygargus) that possess up to 14 B chromosomes to investigate the presence and expression of genes on supernumerary chromosomes. RESULTS: Here, we describe a 2 Mbp region homologous to cattle chromosome 3 and containing TNNI3K (partial), FPGT, LRRIQ3 and a large gene-sparse segment on B chromosomes of the Siberian roe deer. The presence of the copy of the autosomal region was demonstrated by B-specific cDNA analysis, PCR assisted mapping, cattle bacterial artificial chromosome (BAC) clone localization and quantitative polymerase chain reaction (qPCR). By comparative analysis of B-specific and non-B chromosomal sequences we discovered some B chromosome-specific mutations in protein-coding genes, which further enabled the detection of a FPGT-TNNI3K transcript expressed from duplicated genes located on B chromosomes in roe deer fibroblasts. CONCLUSIONS: Discovery of a large autosomal segment in all B chromosomes of the Siberian roe deer further corroborates the view of an autosomal origin for these elements. Detection of a B-derived transcript in fibroblasts implies that the protein coding sequences located on Bs are not fully inactivated. The origin, evolution and effect on host of B chromosomal genes seem to be similar to autosomal segmental duplications, which reinforces the view that supernumerary chromosomal elements might play an important role in genome evolution
Pinniped Karyotype Evolution Substantiated by Comparative Chromosome Painting of 10 Pinniped Species (Pinnipedia, Carnivora)
Numerous Carnivora karyotype evolution investigations have been performed by classical and molecular cytogenetics and were supplemented by reconstructions of the Ancestral Carnivora Karyotype (ACK). However, the group of Pinnipedia was not studied in detail. Here we reconstruct pinniped karyotype evolution and refine ACK using published and our new painting data for 10 pinniped species. The combination of human (HSA) and domestic dog (CFA) whole-chromosome painting probes was used for the construction of the comparative chromosome maps for species from all three pinniped families: Odobenidae– Odobenus rosmarus Linnaeus, 1758, Phocidae – Phoca vitulina Linnaeus, 1758, Pusa sibirica Gmelin, 1788, Erignathus barbatus Erxleben, 1777, Phoca largha Pallas, 1811, Phoca hispida Schreber, 1775 and Otariidae – Eumetopias jubatus Schreber, 1775, Callorhinus ursinus Linnaeus, 1758, Phocarctos hookeri Gray, 1844, Arctocephalus forsteri Lesson, 1828. HSA and CFA autosome painting probes have delineated 32 and 68 conservative autosome segments in the studied genomes. The comparative painting in Pinnipedia supports monophyletic origin of pinnipeds, shows that pinniped karyotype evolution was characterized by slow rate of genome rearrangements (less then one rearrangement per 10 million years), provides strong support for refined structure of ACK with 2n = 38 and specifies plausible order of dog chromosome synthenic segments on ancestral Carnivora chromosomes. The heterochromatin, telomere and ribosomal DNA distribution was studied in all 10 species
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Development and Application of Camelid Molecular Cytogenetic Tools
Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular
importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human-camel zoo-fluorescence
in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome
by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The
genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were
ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no
markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical
cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal
translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as
comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small
LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical
cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly.Keywords: FISH, BAC library, Translocation, Cytogenetics, Minute chromosome, Alpac
Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi
The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification. </p
A Molecular Phylogeny of Living Primates
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species
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