NONRANDOM DISTRIBUTION OF GENES WITH SEX-BIASED EXPRESSION IN THE CHICKEN GENOME

Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens

Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p < 0.05) enriched, which were limb development, inner ear development, positive regulation of dendrite development, the KEGG pathway the TGF-beta signaling pathway, and melanogenesis (p < 0.05). These pathways are related to morphological maintenance and growth of the tissues. In addition, the SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r ² = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.

Sex Chromosome Dosage Compensation in Heliconius Butterflies: Global yet Still Incomplete?

The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit “incomplete” sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius, resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.

Variation in the X:Autosome Distribution of Male-Biased Genes among Drosophila melanogaster Tissues and Its Relationship with Dosage Compensation

Genes that are expressed differently between males and females (sex-biased genes) often show a nonrandom distribution in their genomic location, particularly with respect to the autosomes and the X chromosome. Previous studies of Drosophila melanogaster found a general paucity of male-biased genes on the X chromosome, although this is mainly limited to comparisons of whole flies or body segments containing the reproductive organs. To better understand the chromosomal distribution of sex-biased genes in various tissues, we used a common analysis framework to analyze microarray and RNA sequence data comparing male and female gene expression in individual tissues (brain, Malpighian tubule, and gonads), composite structures (head and gonadectomized carcass), and whole flies. Although there are relatively few sex-biased genes in the brain, there is a strong and highly significant enrichment of male-biased genes on the X chromosome. A weaker enrichment of X-linked male-biased genes is seen in the head, suggesting that most of this signal comes from the brain. In all other tissues, there is either no departure from the random expectation or a significant paucity of male-biased genes on the X chromosome. The brain and head also differ from other tissues in that their male-biased genes are significantly closer to binding sites of the dosage compensation complex. We propose that the interplay of dosage compensation and sex-specific regulation can explain the observed differences between tissues and reconcile disparate results reported in previous studies.

Sex-Biased Expression of Young Genes in Silurana (Xenopus) tropicalis

Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog Silurana (Xenopus)tropicalis. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.

Gene duplication and the genome distribution of sex-biased genes

In species that have two sexes, a single genome encodes two morphs, as each sex can be thought of as a distinct morph. This means that the same set of genes are differentially expressed in the different sexes. Many questions emanate from this statement. What proportion of genes contributes to sexual dimorphism? How do they contribute to sexual dimorphism? How is sex-biased expression achieved? Which sex and what tissues contribute the most to sex-biased expression? Do sex-biased genes have the same evolutionary patterns as nonbiased genes? We review the current data on sex-biased expression in species with heteromorphic sex chromosomes and comment on the most important hypotheses suggested to explain the origin, evolution, and distribution patterns of sex-biased genes. In this perspective we emphasize how gene duplication serves as an important molecular mechanism to resolve genomic clashes and genetic conflicts by generating sex-biased genes, often sex-specific genes, and contributes greatly to the underlying genetic basis of sexual dimorphism.

Slcyt, a newly identified sex-linked gene, has recently moved onto the X chromosome in Silene latifolia (Caryophyllaceae)

The sex chromosomes of the plant species Silene latifolia (white campion) are very young (only 5-10 My old), and all 11 X-linked genes so far described have Y-linked homologues. Theory predicts that X chromosomes should accumulate a nonrandom set of genes. However, little is known about the importance of gene movements between the X and the autosomes in plants, or in any very young sex chromosome system. Here, we isolate from cDNA a new gene, Slcyt, on the S. latifolia X, which encodes a cytochrome B protein. We genetically mapped SlCyt and found that it is located approximately 1 cM from the pseudoautosomal region. Genes in this region of the X chromosome have low divergence values from their homologous Y-linked genes, indicating that the X only recently stopped recombining with the Y. Genetic mapping in Silene vulgaris suggests that Slcyt originally belonged to a different linkage group from that of the other S. latifolia X-linked genes. Silene latifolia has no Y-linked homologue of Slcyt, and also no autosomal paralogues seem to exist. Slcyt moved from an autosome to the X very recently, as the Cyt gene is also X linked in Silene dioica, the sister species to S. latifolia, but is probably autosomal in Silene diclinis, implying that a translocation to the X probably occurred after the split between S. diclinis and S. latifolia/S. dioica. Diversity at Slcyt is extremely low (pi(syn) = 0.16%), and we find an excess of high frequency-derived variants and a negative Tajima's D, suggesting that the translocation was driven by selection.

Fast-X on the Z: rapid evolution of sex-linked genes in birds

Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This "fast-X effect" should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW), where analogous arguments would predict a fast-Z effect. We aligned 2.8 Mb of orthologous protein-coding sequence of zebra finch and chicken from 172 Z-linked and 4848 autosomal genes. Zebra finch data were in the form of EST sequences from brain cDNA libraries, while chicken genes were from the draft genome sequence. The dN/dS ratio was significantly higher for Z-linked (0.110) than for all autosomal genes (0.085; P=0.002), as well as for genes linked to similarly sized autosomes 1-10 (0.0948; P=0.04). This pattern of fast-Z was evident even after we accounted for the nonrandom distribution of male-biased genes. We also examined the nature of standing variation in the chicken protein-coding regions. The ratio of nonsynonymous to synonymous polymorphism (pN/pS) did not differ significantly between genes on the Z chromosome (0.104) and on the autosomes (0.0908). In conjunction, these results suggest that evolution proceeds more quickly on the Z chromosome, where hemizygous exposure of beneficial nondominant mutations increases the rate of fixation.