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Shetty, Swathi; Griffin, Darren K.; Graves, Jennifer A. Marshall

doi:10.1023/a:1009278914829

Cited by 233 publications

(58 citation statements)

References 18 publications

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“…In ratites, sex chromosomes are either largely homomorphic or only show limited differentiation, with recombination occurring over most of the Z and the W chromosomes (Tsuda et al 2007). As sex chromosomes are fully syntenic across Aves (Shetty et al 1999; Nanda et al 2008), this makes it possible to compare sex-specific expression levels of Z-linked genes prior to (Paleognathae) and subsequent to (Neognathae) cessation of recombination and sex chromosome divergence.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers

Uebbing

Künstner

Mäkinen

et al. 2013

Genome Biology and Evolution

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Sex chromosome divergence, which follows the cessation of recombination and degeneration of the sex-limited chromosome, can cause a reduction in expression level for sex-linked genes in the heterozygous sex, unless some mechanisms of dosage compensation develops to counter the reduction in gene dose. Because large-scale perturbations in expression levels arising from changes in gene dose might have strong deleterious effects, the evolutionary response should be strong. However, in birds and in at least some other female heterogametic organisms, wholesale sex chromosome dosage compensation does not seem to occur. Using RNA-seq of multiple tissues and individuals, we investigated male and female expression levels of Z-linked and autosomal genes in the collared flycatcher, a bird for which a draft genome sequence recently has been reported. We found that male expression of Z-linked genes was on average 50% higher than female expression, although there was considerable variation in the male-to-female ratio among genes. The ratio for individual genes was well correlated among tissues and there was also a correlation in the extent of compensation between flycatcher and chicken orthologs. The relative excess of male expression was positively correlated with expression breadth, expression level, and number of interacting proteins (protein connectivity), and negatively correlated with variance in expression. These observations lead to a model of compensation occurring on a gene-by-gene basis, supported by an absence of clustering of genes on the Z chromosome with respect to the extent of compensation. Equal mean expression level of autosomal and Z-linked genes in males, and 50% higher expression of autosomal than Z-linked genes in females, is compatible with that partial compensation is achieved by hypertranscription from females’ single Z chromosome. A comparison with male-to-female expression ratios in orthologous Z-linked genes of ostriches, where Z–W recombination still occurs, suggests that male-biased expression of Z-linked genes is a derived trait after avian sex chromosome divergence.

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Section: Resultsmentioning

confidence: 99%

Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers

Uebbing

Künstner

Mäkinen

et al. 2013

Genome Biology and Evolution

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“…The 19 loci are located on 15 different chromosomes in the chicken genome [40], and they are likely to be unlinked in most or all avian lineages given the general conservation of avian karyotypes [41]. There was clear evidence that one locus ( GH1 ) underwent a gene duplication within birds [42]; a single GH1 paralog was included for the taxa (Passeriformes) with two copies.…”

Section: Methodsmentioning

confidence: 99%

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Yuri

Kimball

Harshman³

et al. 2013

Biology

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Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

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“…The suppression of recombination favored the accumulation of gene mutations on the sex-specific chromosome, leading to numerous deletions of the functionally inactivated genes and accumulation of repetitive DNA sequences (6,7). The mammalian Y chromosome and avian W chromosome became highly degenerated and extensively heteochromatized, with the exception of monotremes and palaeognathous birds, which have less differentiated sex chromosomes (8)(9)(10)(11)(12)(13). The human Y chromosome still contains 27 homologues of X-linked single-copy genes and pseudogenes (14), and chicken has also the Z and W forms of six ''gametologous'' genes, which arose by the cessation of recombination because of sexchromosome differentiation, ATP5A1, CHD1, HINTZ, PKCI, SPIN, and UBA2 (15)(16)(17).…”

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confidence: 99%

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes

Matsubara

Tarui²,

Toriba

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

281

399

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All snake species exhibit genetic sex determination with the ZZ͞ZW type of sex chromosomes. To investigate the origin and evolution of snake sex chromosomes, we constructed, by FISH, a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 109 cDNA clones. Eleven of the 109 clones were localized to the Z chromosome. All human and chicken homologues of the snake Z-linked genes were located on autosomes, suggesting that the sex chromosomes of snakes, mammals, and birds were all derived from different autosomal pairs of the common ancestor. We mapped the 11 Z-linked genes of E. quadrivirgata to chromosomes of two other species, the Burmese python (Python molurus bivittatus) and the habu (Trimeresurus flavoviridis), to investigate the process of W chromosome differentiation. All and 3 of the 11 clones were localized to both the Z and W chromosomes in P. molurus and E. quadrivirgata, respectively, whereas no cDNA clones were mapped to the W chromosome in T. flavoviridis. Comparative mapping revealed that the sex chromosomes are only slightly differentiated in P. molurus, whereas they are fully differentiated in T. flavoviridis, and E. quadrivirgata is at a transitional stage of sex-chromosome differentiation. The differentiation of sex chromosomes was probably initiated from the distal region on the short arm of the protosex chromosome of the common ancestor, and then deletion and heterochromatization progressed on the sex-specific chromosome from the phylogenetically primitive boids to the more advanced viperids.comparative map ͉ chromosome homology ͉ FISH ͉ sex-determining gene ͉ reptile A ll snake species are subject to genetic sex determination with sex chromosomes, as are mammals and birds, and they have female heterogamety (ZZ males and ZW females). Comparative gene mapping between human and chicken revealed that human XX͞XY and chicken ZZ͞ZW sex chromosomes have no homologies (1, 2), suggesting that the sex chromosomes of mammals and birds were derived from different pairs of autosomes of the common ancestor. Beçak et al. (3) found that there is close karyological similarity between snakes and birds, such as distinct differentiation of macro-and microchromosomes and constant occurrence of ZW-type sex chromosomes. This finding leads us to predict the presence of homology between ophidian and avian sex chromosomes. However, no attempts have yet been made to investigate the conservation of the linkage homologies of snake chromosomes to human and chicken chromosomes by comparative gene mapping, although this approach would provide fundamental information on the genome evolution and the origin of sex-chromosome differentiation in amniotes. In another study (4), we constructed a preliminary cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 52 EST clones, which were isolated from the cDNA library of the brain tissue and were identified as snake homologues of human and chicken orthologous genes by a search of the DNA database. Of 52 EST clones, two genes, T...

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Cited by 233 publications

References 18 publications

Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers

Transcriptome Sequencing Reveals the Character of Incomplete Dosage Compensation across Multiple Tissues in Flycatchers

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes

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