Chromosome Evolution in Perissodactyla

Trifonov, Vladimir A.; Musilová, Petra; Kulemsina, A.I.

doi:10.1159/000339900

Cited by 19 publications

(22 citation statements)

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“…As shown in Fig. 3 , from the evolutionary point of view, ERE1 loci can be classified in three groups: elements which are conserved in all species of the genus Equus (53 loci) and thus were inserted in a common ancestor of all extant equids, at least 3.8 Ma ago (Mya); elements which are conserved in all analyzed horses ( E. caballus and E. przewalskii ) but absent in the other Equus species (25 loci), thus inserted after the separation of the horse lineage, that is about 3.8 Mya [ 58 , 59 ]; elements which are present in E. caballus only (two loci: 11 and 35 in Fig. 2 ) and therefore were probably inserted after the separation of the two horse species.…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression

Santagostino¹,

Khoriauli²,

Gamba³

et al. 2015

BMC Genet

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BackgroundIn mammals, an important source of genomic variation is insertion polymorphism of retrotransposons. These may acquire a functional role when inserted inside genes or in their proximity. The aim of this work was to carry out a genome wide analysis of ERE1 retrotransposons in the horse and to analyze insertion polymorphism in relation to evolution and function. The effect of an ERE1 insertion in the promoter of the myostatin gene, which is involved in muscle development, was also investigated.ResultsIn the horse population, the fraction of ERE1 polymorphic loci is related to the degree of similarity to their consensus sequence. Through the analysis of ERE1 conservation in seven equid species, we established that the level of identity to their consensus is indicative of evolutionary age of insertion. The position of ERE1s relative to genes suggests that some elements have acquired a functional role. Reporter gene assays showed that the ERE1 insertion within the horse myostatin promoter affects gene expression. The frequency of this variant promoter correlates with sport aptitude and racing performance.ConclusionsSequence conservation and insertion polymorphism of ERE1 elements are related to the time of their appearance in the horse lineage, therefore, ERE1s are a useful tool for evolutionary and population studies. Our results suggest that the ERE1 insertion at the myostatin locus has been unwittingly selected by breeders to obtain horses with specific racing abilities. Although a complex combination of environmental and genetic factors contributes to athletic performance, breeding schemes may take into account ERE1 insertion polymorphism at the myostatin promoter.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0281-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…3 Phylogenetic tree of equids. The time of insertion of each one of the 80 ERE1s is marked on the phylogenetic tree (adapted from [ 58 , 59 ]). ERE1 loci are classified according to the percentage of identity to the consensus sequence, the fraction of inserted loci in each class of identity is shown.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression

Santagostino¹,

Khoriauli²,

Gamba³

et al. 2015

BMC Genet

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“…Synteny HSA 12/22/18 was suggested to be a cytogenetic character linking Carnivora and Cetartiodactyla [ 13 , 42 , 44 ]. It was also suggested that there is an association HSA 1q/10q (with HSA1q being really small size—HSA1q42.1–q43) that is common for all Boreutherian mammals [ 48 ]. However we did not see the segment of 1q on the corresponding pinniped chromosomes (OROS1, EJUB11, PSIB7) and it is likely that the size of this HSA1q segment is at the threshold of chromosome painting resolution.…”

Section: Discussionmentioning

confidence: 99%

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora)

et al. 2016

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Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.

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“…All analyzed members of the family have a potentially functional KIR3DL gene, two KIR pseudogenes and a KIR-ILTA hybrid gene. Observations on a rapid karyotype evolution [18] supported by data on rapid evolution of insertion sequences [19] suggested that genomes of the Equidae are rapidly evolving. Within immunity-related genes, NKR genes belong to a very variable and little conservative group [2].…”

Section: Discussionmentioning

confidence: 94%

“…Among them, the family Equidae consisting of a single genus, Equus [16] with different free-living and domesticated species exposed to a variety of pathogens in different habitats is a suitable model for analyzing diversity and evolution of immunity-related genes [17]. It is a rapidly evolving mammalian family, both at the karyotype [18] and molecular [19] level. Therefore, the Equidae might also be interesting models for studying evolution of NKR genes.…”

Section: Introductionmentioning

confidence: 99%

Natural Killer Cell Receptor Genes in the Family Equidae: Not only Ly49

Futas

Hořín

2013

PLoS ONE

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Natural killer (NK) cells have important functions in immunity. NK recognition in mammals can be mediated through killer cell immunoglobulin-like receptors (KIR) and/or killer cell lectin-like Ly49 receptors. Genes encoding highly variable NK cell receptors (NKR) represent rapidly evolving genomic regions. No single conservative model of NKR genes was observed in mammals. Single-copy low polymorphic NKR genes present in one mammalian species may expand into highly polymorphic multigene families in other species. In contrast to other non-rodent mammals, multiple Ly49-like genes appear to exist in the horse, while no functional KIR genes were observed in this species. In this study, Ly49 and KIR were sought and their evolution was characterized in the entire family Equidae. Genomic sequences retrieved showed the presence of at least five highly conserved polymorphic Ly49 genes in horses, asses and zebras. These findings confirmed that the expansion of Ly49 occurred in the entire family. Several KIR-like sequences were also identified in the genome of Equids. Besides a previously identified non-functional KIR-Immunoglobulin-like transcript fusion gene (KIR-ILTA) and two putative pseudogenes, a KIR3DL-like sequence was analyzed. In contrast to previous observations made in the horse, the KIR3DL sequence, genomic organization and mRNA expression suggest that all Equids might produce a functional KIR receptor protein molecule with a single non-mutated immune tyrosine-based inhibition motif (ITIM) domain. No evidence for positive selection in the KIR3DL gene was found. Phylogenetic analysis including rhinoceros and tapir genomic DNA and deduced amino acid KIR-related sequences showed differences between families and even between species within the order Perissodactyla. The results suggest that the order Perissodactyla and its family Equidae with expanded Ly49 genes and with a potentially functional KIR gene may represent an interesting model for evolutionary biology of NKR genes.

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Chromosome Evolution in Perissodactyla

Cited by 19 publications

References 50 publications

Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression

Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora)

Natural Killer Cell Receptor Genes in the Family Equidae: Not only Ly49

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