Qi Zhou
1)​ How does the mammalian Y chromosome degenerate?
XY and ZW sex chromosome systems have independent evolutionary histories in different lineages. With few exceptions, Y and W chromosomes don't have homologous recombination along almost the entire chromosome, and have lost most of the functional genes. How does the Y or W degenerates remains largely unknown, because the sequenced human or Drosophila Y chromosomes bear few traces of their evolution. I identifed the first mammalian 'neo-sex' system in a deer species black muntjac to study this question. This species has evolved a particular male-specific inversion on one autosome within 1 million years, forming a very young 'neo-Y' chromosome with an ongoing degeneration process.
I. Evolution of Vertebrate Sex Chromosomes
2) Evolution atlas of avian sex chromosomes
This is one of the first 'Genomes of 10,000 species' (G10K) projects involving collabration of more than 70 groups all over the world, where we studied genomes of a total of 48 bird species spanning the entire avian phylogeny. The data was produced in Beijing Genomic Institute, and I lead a group of bioinformaticians there and uncoverred a complex history of recombination suppression between Z and W chromosomes of birds, which reveals a clear pattern of 'evolutionary strata'. This work is currently under review by Science.
II. Evolution of Drosophila Neo-sex Systems
Several Drosophila species have also formed 'neo-sex' systems by the fusion of autosomes to the ancestral sex chromosomes at different evolutionary time points, providing a timecourse of evolving young sex chromosomes. I use next-generation sequencing technology, assemble and annotate the genomes of these Drosophila species, accompanied by the analyses of the transcriptomes of multiple tissues.
1) Drosophila albomicans
Males of this species have a characteristic silver patch on the fronhead, and a pair of autosomes comprising 40% of the entire genome that has fused to the ancestral X and Y chromosome pair. This system is only 0.12 million years old, and is the youngest and largest neo-sex system reported to date. Besides, this species also has B-chromosomes, whose numbers within cells affect the numbers of offsprings. By analyzing its genome, I found only less than 1% of the neo-Y genes have become non-functional, and B chromosomes probably originated during the fusion creating the neo-sex chromosome pair. However, after studying the transcriptomes of this species, we found 30% of the neo-Y genes have been down-regulated for their expression, suggesting regulatory changes predate the protein sequence changes during the Y degeneration.
2) Drosophila miranda
D. miranda has a neo-sex system aged 1 million years and has been extensively studied by my postdoctoral advisor Dr. Doris Bachtrog in the past ten years. After I joined Doris' lab, I developed novel algorithsms and assembled the neo-X and neo-Y chromosome in separate for this species. We found 40% of the neo-Y genes have become non-functional. Interestingly, a lot of genes also show robust evidence of 'masculinization' in their transcriptomes of male-specific tissues, indicating the couteracting forces of adaptive evolution and degeneration on the evolving Y chromosome. Through collabrating with my colleage Dr. Raquel Assis, we show genes on the X chromosomes in contrast show patterns of 'demasculinization'. These patterns may together be explained by forces of sexual antagonism acting on the evolving sex chromosomes.
III. Evolution of New Genes in Drosophila
The muntjac picture is from Michela Botta.
The interest in the orgin of genetic novelty can be dated back to the time of Darwins. My Ph.D. mentor Dr. Wen Wang has developed experimental methods to systematically study this quetion in multiple Drosophila species. Comparative genomics affords a more powerful tool to address the patterns and mechanisms of new gene orignation at a whole genome level. I studied genomes of six different Drosophila species and identified all the species or lineage specific new genes of different ages. I found contrary to the traditional view, genes de novo originated from non-coding sequences contribute 12% of the entire novel genes, suggesting this mechanism plays an important role.
