Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome

Abstract

Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.

Keywords: crustacean; dosage compensation; gene expression; sex chromosome; sexual dimorphism.

Fig. 1.

—Transcriptome quality and sex-biased genes. (A) Shows the quality of the published transcriptome (Valenzuela-Miranda et al. 2014), the transcripts from the genome made recently available by the Korean Polar Institute (2018), and our own transcriptome assembly based on BUSCO completeness of 1,066 highly conserved single-copy orthologs. (B) Shows the numbers of sex-biased genes in heads and gonads and the overlap between the tissues.

Fig. 2.

—Z chromosome identification and comparison of gene expression patterns with the autosomes. (A) Log₂(Female:Male genomic coverage) of transcripts. Median log₂(Female:Male coverage) shown as the central black dashed line. Median coverage ±1 are also shown as vertical black dashed lines. Cutoff for Z-chromosome coverage shown as dashed red line. Transcripts to the left of the dashed red line are assigned to the Z chromosome, and right of the dashed red line are assigned to autosomes. (B) Gene expression of females (pink) and males (blue) on the autosomes (“A”) and the Z chromosome (“Z”) in gonads. (C) Gene expression of females (pink) and males (blue) on the autosomes (“A”) and the Z chromosome (“Z”) in heads. (D) Female-over-male (“F/M”) expression ratios compared for the autosomes (“A,” gray) and the Z chromosome (“Z,” green) in gonads. (E) Female-over-male (“F/M”) expression ratios compared for the autosomes (“A,” gray) and the Z chromosome (“Z,” green) in heads. Wilcoxon test, *P value < 0.05, **P value < 0.01.

Fig. 3.

—Identification of undifferentiated ZW region. (A) Coverage and proportion of ZW SNPs on each scaffold. Scaffolds below the horizontal red dashed line are defined as Z-specific based on their log₂(female:male) coverage ratio. Autosomal scaffolds are above the horizontal red dashed line and to the left of the vertical red dashed line. Young Z scaffolds are above the horizontal red dashed line and to the right of the vertical dashed line, and are defined by having >20% of the SNPs consistent with ZW-inheritance. The number of transcripts in each category is given in parentheses. (B) The proportion of sex-chromosome consistent SNPs in the RNA data that are also consistent in the DNA sequencing data set. Only SNPs on scaffolds with >20% of SNPs supporting a ZW karyotype in the RNA data set (putative young ZW strata) were considered. *** denotes a significant enrichment in the proportion of ZW-consistent SNPs in the RNA that were also ZW-consistent in the DNA, compared with the same proportion for all SNPs identified in the RNA (P < 2.2×10⁻¹⁶).

Fig. 4.

—Testing for sex-linkage of Masc, a gene known to be involved in sex determination. qPCR amplification results are shown for a Z-linked gene annotation (Art-3923), for an autosomal control (Art-11161), and for Masc.