Abstract
The parthenogenetic marbled crayfish (Procambarus virginalis) sparked interest within the scientific community due to its unique features. Its polyploid and monoclonal genome, high environmental adaptability and phenotypic diversity made the marbled crayfish a suitable laboratory model for genomics, epigenetics and ecology research. The previously established marbled crayfish genome sequence of 3.5 Gbp represents a highly fragmented draft assembly. Initial comparative genomic analyses resulted in confirmation of P. virginalis genome origination from the sexually reproducing freshwater crayfish P. fallax. However, in-depth genomic analysis and interspecies genome comparisons require further refinement of the fragmented genome reference of the marbled crayfish. In this PhD thesis, the first refinement of the marbled crayfish genome has been performed with application of the PacBio Single Molecule Real Time (SMRT) sequencing technology. The new and improved genome assembly of the marbled crayfish resulted in 3.7 Gbp of sequence length and an N50 of 144kb. The refined genome assembly enabled searching parental haplotypes and understanding species origination. The absence of evidence for loss of heterozygosity in the various monoclonal marbled crayfish generations suggests the lack of recombination process during oogenesis. Thus, marbled crayfish suggest to be apomictic parthenogens which are characterized by generating identical copies of the maternal genotype. Moreover, despite of the limited genome variability, monoclonal marbled crayfish genomes consisted of population-specific genetic polymorphisms within the global population. Comparative genomic analysis between geographically distant populations resulted in the identification of population-specific mutational signatures. The calculation of genomic variability of marbled crayfish from the growing population in Lake Reilingen allowed to estimate population dynamics. Thus, the population in Lake Reilingen demonstrates a rapid growth, following the density-independent exponential model. This PhD thesis provides fundamental insights into marbled crayfish research, particularly via making use of an improved genome assembly for comparative genomic analyses, epigenetic studies, and for research on the evolution and genomic adaptation to asexuality.
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