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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2015)
Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species.
    Cover page: Partial Dosage Compensation in Strepsiptera, a Sister Group of Beetles
    • Article
    • Peer Reviewed
    Berkeley Research Impact Initiative (BRII) (2017)
    Sex-chromosomes have formed repeatedly across Diptera from ordinary autosomes, and X-chromosomes mostly conserve their ancestral genes. Y-chromosomes are characterized by abundant gene-loss and an accumulation of repetitive DNA, yet the nature of the gene repertoire of fly Y-chromosomes is largely unknown. Here we trace gene-content evolution of Y-chromosomes across 22 Diptera species, using a subtraction pipeline that infers Y genes from male and female genome, and transcriptome data. Few genes remain on old Y-chromosomes, but the number of inferred Y-genes varies substantially between species. Young Y-chromosomes still show clear evidence of their autosomal origins, but most genes on old Y-chromosomes are not simply remnants of genes originally present on the proto-sex-chromosome that escaped degeneration, but instead were recruited secondarily from autosomes. Despite almost no overlap in Y-linked gene content in different species with independently formed sex-chromosomes, we find that Y-linked genes have evolved convergent gene functions associated with testis expression. Thus, male-specific selection appears as a dominant force shaping gene-content evolution of Y-chromosomes across fly species.
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2017)

      Abstract

      Sex Chromosome Evolution in Insects

      by

      Shivani Mahajan

      Doctor of Philosophy in Integrative Biology

      University of California, Berkeley

      Professor Doris Bachtrog, Chair

      Sex chromosomes play a role in sex determination in several organisms, ranging from humans and other mammals to flies, and present unique characteristics that distinguish them from autosomes. However, the underlying evolutionary forces that drive sex chromosome evolution and the molecular processes and mechanisms shaping their unusual characteristics are poorly understood, even in well-studied organisms like Drosophila melanogaster and humans. In this dissertation, I studied several aspects of sex chromosome evolution, including the mechanism of dosage compensation, Y degeneration and gene content evolution of Y chromosomes, sequence evolution of recently formed neo-sex chromosomes, and changes of the chromatin landscape in species with newly evolved sex chromosomes, in both model and non-model organisms.

      X and Y chromosomes are derived from a pair of ordinary autosomes. Y chromosomes do not recombine, which leads to their degeneration and causes them to lose genes. This creates a gene-dose imbalance for X-linked genes in males compared to females, and also compared to autosomes, and different organisms have evolved different mechanisms to compensate for this imbalance. While in humans one of the two X chromosomes in females is randomly inactivated in different cells, Drosophila melanogaster males hyper-transcribe genes on their single X chromosome. In the first chapter, I tested for dosage compensation in the order Strepsiptera, which is a sister group of Coleoptera (beetles). Using DNA-seq and RNA-seq data, I showed that the species Xenos vesparum shares an X chromosome with the flour beetle Tribolium that is fully dosage compensated. However, X. vesparum also contains a more recently evolved X chromosome that is autosomal in Tribolium, and which has evolved only partial dosage compensation.

      Y chromosomes degenerate and contain very few genes. They also accumulate repetitive DNA, which makes their sequencing and assembly extremely difficult. In the second chapter I developed a bioinformatics pipeline to extract Y-linked coding sequences using DNA-seq and RNA-seq data from males and females of a species, without having to assemble the repetitive Y chromosome. I applied this pipeline to several Diptera flies, to characterize and study their Y gene content. I showed that there was no overlap between Y-linked genes in different Dipterans, and that different species had convergently acquired genes with testis-specific functions, highlighting the importance of male-specific selection in driving the evolution of Y gene content.

      Species with newly evolved neo-sex chromosomes, such as Drosophila miranda, provide a unique opportunity to study sex chromosome evolution, since its neo-Y still retains significant sequence identity to its former homolog, the neo-X chromosome, and it also still contains thousands of genes. However, this also makes the neo-Y chromosome particularly difficult to assemble using short read technology alone, due to the inability to unambiguously assign sequencing reads to either the neo-X or the neo-Y, and also due to the repetitive nature of the neo-Y in general. In the third chapter, I used Single Molecule Sequencing (Pacbio) and Chromatin Conformation Capture along with Illumina whole genome shot-gun sequencing to build a high quality genome assembly for Drosophila miranda. I showed that the neo-Y chromosome has greatly increased in size by almost 3-fold, compared to the neo-X chromosome, due to the accumulation of repetitive sequences, but also due to the expansion of some male-specific genes on the neo-Y. This assembly provides the basis for future functional studies of sex chromosome evolution in this species.

      A large proportion of the genome in Drosophila miranda is repetitive and heterochromatic (~43%). The different chromatin compartments are established during early embryonic development, but very little is known about how this happens at the molecular level, and what primary sequences target parts of the genome to establish a heterochromatic conformation. In the fourth chapter I studied heterochromatin establishment in D.miranda during early development using single embryo ChIP-seq. I showed that males experience a delay in the establishment of the heterochromatic histone mark H3K9me3 compared to females. I also investigated signatures of H3K9me3 spreading near euchromatic transposable element (TE)/repeat insertions and showed that this signal is more pronounced for TEs that are targeted by maternally inherited piRNAs, suggesting that they may play an important role in the establishment of heterochromatin.

        Cover page: Sex Chromosome Evolution in Insects
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2019)
        Widespread loss of genes on the Y is considered a hallmark of sex chromosome differentiation. Here we show that the initial stages of Y evolution are driven by massive amplification of distinct classes of genes. The neo-Y chromosome of Drosophila miranda initially contained about 3,000 protein-coding genes, but has gained over 3,200 genes since its formation about 1.5 million years ago primarily by tandem amplification of protein-coding genes ancestrally present on this chromosome. We show that distinct evolutionary processes may account for this drastic increase in gene number on the Y. Testis-specific and dosage-sensitive genes appear to have amplified on the Y to increase male fitness. A distinct class of meiosis-related multi-copy Y genes independently co-amplified on the X, and their expansion is probably driven by conflicts over segregation. Co-amplified X/Y genes are highly expressed in testis, enriched for meiosis and RNA interference functions and are frequently targeted by small RNAs in testis. This suggests that their amplification is driven by X versus Y antagonism for increased transmission, where sex chromosome drive suppression is probably mediated by sequence homology between the suppressor and distorter through the RNA interference mechanism. Thus, our analysis suggests that newly emerged sex chromosomes are a battleground for sexual and meiotic conflict.
          Cover page: Massive gene amplification on a recently formed Drosophila Y chromosome.
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2013)
          Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.
            Cover page: Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2016)
            Alternative pre-mRNA splicing ("AS") greatly expands proteome diversity, but little is known about the evolutionary landscape of AS in Drosophila and how it differs between embryonic and adult stages or males and females. Here we study the transcriptomes from several tissues and developmental stages in males and females from four species across the Drosophila genus. We find that 20-37% of multi-exon genes are alternatively spliced. While males generally express a larger number of genes, AS is more prevalent in females, suggesting that the sexes adopt different expression strategies for their specialized function. While the number of total genes expressed increases during early embryonic development, the proportion of expressed genes that are alternatively spliced is highest in the very early embryo, before the onset of zygotic transcription. This indicates that females deposit a diversity of isoforms into the egg, consistent with abundant AS found in ovary. Cluster analysis by gene expression ("GE") levels shows mostly stage-specific clustering in embryonic samples, and tissue-specific clustering in adult tissues. Clustering embryonic stages and adult tissues based on AS profiles results in stronger species-specific clustering, suggesting that diversification of splicing contributes to lineage-specific evolution in Drosophila. Most sex-biased AS found in flies is due to AS in gonads, with little sex-specific splicing in somatic tissues.
              Cover page: Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
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