Date of Graduation
Eberly College of Arts and Sciences
Identifying the sex-determination region (SDR) and other genomic features of sex chromosomes are of great importance in the studies of the evolution of sex. However, the process of accurately identifying the size and location of the SDR is often difficult, even when a genomic sequence is available. This usually is hindered by large repetitive elements and a lack of recombination in the SDR. In this thesis, I assemble sex chromosomes with whole genomic sequencing data, identify SDRs and explore their genomic features in two sister species from the Salicaceae family. I also develop an interpretation of the lability of the sex configuration in the two species. In Chapter 2, I use quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the SDR in a reference genome derived a female Salix purpurea clone. I show that the SDR in S. purpurea has a female heterogametic (ZW) system on chromosome 15. The SDR is inferred to be between 5 to 7 Mb long and overlapping with the centromere. This SDR has several classic features like reduced recombination and high structural polymorphism. Intriguingly, chromosome 19 contains sex-associated markers, which raises the possibility of a translocation of the SDR within the Salicaceae lineage. In Chapter 3, I improve the quality of assembly of sex chromosomes in S. purpurea with long-reads sequencing data and a modified map. Using an improved assembly of the SDR, I show that two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb stretches of highly conserved homologous sequences among the four arms in the female-specific regions of the SDR. Comparison to the genome of a closely related species S. suchowensis provides evidence for gene conversion occurring among the palindrome arms. The hypothesis of the translocation of the SDR within the Salicaceae could not be rejected. In Chapter 4, I use a similar strategy from Chapter 3 to study the SDR of a male Populus trichocarpa clone. I show that the SDR in P. trichocarpa has a male heterogametic (XY) system on chromosome 19. A cluster of inverted repeats that are homologous with a response regulator gene is present in the male-specific region in the SDR. This research provides important genomic resources for futures studies in these two species as well as the evolution of SDRs in the Salicaceae.
Zhou, Ran, "Evolutionary genomics of dynamic sex chromosomes in the Salicaceae" (2020). Graduate Theses, Dissertations, and Problem Reports. 7649.