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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

ABSTRACT: The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.

SUBMITTER: Bidon T

PROVIDER: S-EPMC4524476 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

Bidon Tobias T Schreck Nancy N Hailer Frank F Nilsson Maria A MA Janke Axel A

Genome biology and evolution 20150527 7

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and ...[more]

PMID: 26019166

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Project description:Polar bears in captivity can be exposed to opportunistic pathogens not present in their natural environments. A 4-month-old polar bear (Ursus maritimus) living in an isolated enclosure with his mother in the Tierpark Berlin, Berlin, Germany, was suffering from severe abdominal pain, mild diarrhea, and loss of appetite and died in early 2017. Histopathology revealed severe hepatic degeneration and necrosis without evidence of inflammation or inclusion bodies, although a viral infection had been suspected on the basis of the clinical signs. We searched for nucleic acids of pathogens by shotgun high-throughput sequencing (HTS) from genomic DNA and cDNA extracted from tissue and blood. We identified a novel Mastadenovirus and assembled a nearly complete genome from the shotgun sequences. Quantitative PCR (qPCR) revealed that viral DNA was present in various concentrations in all tissues examined and that the highest concentrations were found in blood. Viral culture did not yield cytopathic effects, but qPCR suggested that virus replication was sustained for up to three passages. Positive immunofluorescence staining confirmed that the virus was able to replicate in the cells during early passage. Phylogenetic analysis demonstrated that the virus is highly divergent compared to other previously identified Mastadenovirus members and basal to most known viral clades. The virus was found only in the 4-month-old bear and not in other captive polar bears tested. We surmised, therefore, that the polar bear was infected from an unknown reservoir, illustrating that adenoviral diversity remains underestimated and that cross-species transmission of viruses can occur even under conditions of relative isolation.IMPORTANCE Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined.

Project description:BackgroundThe spatial ecology of individuals often varies within a population or species. Identifying how individuals in different classes interact with their environment can lead to a better understanding of population responses to human activities and environmental change and improve population estimates. Most inferences about polar bear (Ursus maritimus) spatial ecology are based on data from adult females due to morphological constraints on applying satellite radio collars to other classes of bears. Recent studies, however, have provided limited movement data for adult males and sub-adults of both sexes using ear-mounted and glue-on tags. We evaluated class-specific movements and step selection patterns for polar bears in the Chukchi Sea subpopulation during spring.MethodsWe developed hierarchical Bayesian models to evaluate polar bear movement (i.e., step length and directional persistence) and step selection at the scale of 4-day step lengths. We assessed differences in movement and step selection parameters among the three classes of polar bears (i.e., adult males, sub-adults, and adult females without cubs-of-the-year).ResultsAdult males had larger step lengths and less directed movements than adult females. Sub-adult movement parameters did not differ from the other classes but point estimates were most similar to adult females. We did not detect differences among polar bear classes in step selection parameters and parameter estimates were consistent with previous studies.ConclusionsOur findings support the use of estimated step selection patterns from adult females as a proxy for other classes of polar bears during spring. Conversely, movement analyses indicated that using data from adult females as a proxy for the movements of adult males is likely inappropriate. We recommend that researchers consider whether it is valid to extend inference derived from adult female movements to other classes, based on the questions being asked and the spatial and temporal scope of the data. Because our data were specific to spring, these findings highlight the need to evaluate differences in movement and step selection during other periods of the year, for which data from ear-mounted and glue-on tags are currently lacking.

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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

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