Genomic identification and characterization of the pseudoautosomal region in highly
differentiated avian sex chromosomes

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Abstract

The molecular characteristics of the pseudoautosomal region (PAR) of sex chromosomes remain elusive. Despite significant genome-sequencing efforts, the PAR of highly differentiated avian sex chromosomes remains to be identified. Here we use linkage analysis together with whole-genome re-sequencing to uncover the 630-kb PAR of an ecological model species, the collared flycatcher. The PAR contains 22 protein-coding genes and is GC rich. The genetic length is 64 cM in female meiosis, consistent with an obligate crossing-over event. Recombination is concentrated to a hotspot region, with an extreme rate of >700 cM/Mb in a 67-kb segment. We find no signatures of sexual antagonism and propose that sexual antagonism may have limited influence on PAR sequences when sex chromosomes are nearly fully differentiated and when a recombination hotspot region is located close to the PAR boundary. Our results demonstrate that a very small PAR suffices to ensure homologous recombination and proper segregation of sex chromosomes during meiosis.

Abstract

The genetic basis of sex chromosome pseudoautosomal regions (PAR) in organisms with female heterogamety is largely unknown. Smeds et al. provide the first molecular characterization of the PAR in birds with differentiated sex chromosomes and show a potential recombination hotspot and no evidence for strong sexual antagonism in this region.

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An algorithm for progressive multiple alignment of sequences with insertions.

Ari Löytynoja, Nick Goldman (2005)

Dynamic programming algorithms guarantee to find the optimal alignment between two sequences. For more than a few sequences, exact algorithms become computationally impractical, and progressive algorithms iterating pairwise alignments are widely used. These heuristic methods have a serious drawback because pairwise algorithms do not differentiate insertions from deletions and end up penalizing single insertion events multiple times. Such an unrealistically high penalty for insertions typically results in overmatching of sequences and an underestimation of the number of insertion events. We describe a modification of the traditional alignment algorithm that can distinguish insertion from deletion and avoid repeated penalization of insertions and illustrate this method with a pair hidden Markov model that uses an evolutionary scoring function. In comparison with a traditional progressive alignment method, our algorithm infers a greater number of insertion events and creates gaps that are phylogenetically consistent but spatially less concentrated. Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms.

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Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration.

Doris Bachtrog (2013)

The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species and in plants have shed light on the current gene content of the Y chromosome, its origins and its long-term fate. Furthermore, comparative analysis of young and old Y chromosomes has given further insights into the evolutionary and molecular forces triggering Y-chromosome degeneration and into the evolutionary destiny of the Y chromosome.

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Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.

Songlin Chen, Guojie Zhang, Changwei Shao … (2014)

Genetic sex determination by W and Z chromosomes has developed independently in different groups of organisms. To better understand the evolution of sex chromosomes and the plasticity of sex-determination mechanisms, we sequenced the whole genomes of a male (ZZ) and a female (ZW) half-smooth tongue sole (Cynoglossus semilaevis). In addition to insights into adaptation to a benthic lifestyle, we find that the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Notably, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole. Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution. Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'.

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Author and article information

Journal

Journal ID (nlm-ta): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Pub. Group

ISSN (Electronic): 2041-1723

Publication date (Electronic): 07 November 2014

Volume: 5

Electronic Location Identifier: 5448

Affiliations

[1 ]Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University , Norbyvägen 18D, SE-752 36 Uppsala, Sweden

[2 ]Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University , Norbyvägen 18D, SE-752 36 Uppsala, Sweden

[3 ]Department of Biology, Norwegian University of Science and Technology , N-7491 Trondheim, Norway

Author notes

[a ] Hans.Ellegren@ 123456ebc.uu.se

[*]

These authors contributed equally to this work

Article

Publisher Item ID: ncomms6448

DOI: 10.1038/ncomms6448

PMC ID: 4272252

PubMed ID: 25378102

SO-VID: e2236447-bc66-43c0-a9c7-493a906604e0

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Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes

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Most cited references 46

An algorithm for progressive multiple alignment of sequences with insertions.

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration.

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.

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