14 November 2017

Gutekunst, 2017

Gutekunst J. 2017. Clonal genome evolution of the marbled crayfish, Procambarus virginalis. Doctoral thesis, Combined Faculties of Natural Sciences and Mathematics, Ruperto-Carola University Heidelberg. Heidelberg, Germany. 88 pp. https://doi.org/10.11588/heidok.00023501


Marbled crayfish (Procambarus virginalis) are the only freshwater crayfish known to reproduce by cloning (apomictic parthenogenesis). Notably, among genetically identical offspring raised in the same environment, distinct phenotypic differences can be observed. These unique characteristics establish the marbled crayfish as a particularly interesting laboratory model. Additionally, parthenogenetic reproduction enables the marbled crayfish to rapidly spread and form stable populations, which poses a serious threat in many freshwater habitats. A further understanding of this organism requires the accessibility of its 3.5 Gbp large genome sequence.

This doctoral thesis provides the first de novo genome assembly of the marbled crayfish. Multiple shotgun and long jumping distance libraries were generated from one individual female, with a single base coverage of over 100×. Sequencing data was used for a first genome assembly with a length weighted median scaffold size (N50) of over 40 kbp. The estimated genome wide heterozygosity rate of 0.53% is substantially higher compared to other arthropod genomes. Transcriptome data enabled the refinement of genetic structures. Eventually, a total of 87.8% complete and 7.4% fragmented single-copy arthropod orthologs were identified using the benchmarking software BUSCO. Single nucleotide variations were analyzed to verify clonality in geographically isolated populations. Results indicate an evolution from a single origin. Moreover, detailed insights into genotype distributions support the theory of asexual speciation by autopolyploidization. Comparison of three Procambarus species indicates detectable genetic separation between marbled crayfish and the closest relative Procambarus fallax. Automatic annotation of 21,000 genes using the annotation pipeline MAKER provides a detailed overview of genetic features. For example, a cellulase gene was identified which potentially plays a key role in omnivorousness. Genomic data and several online services are provided by a central web resource.

This thesis provides detailed genetic insights into the unknown but very versatile order of decapod crustaceans. Considered economically and ecologically relevant keystone species, a representative genome sequence provides an important resource for future research.

Keywords: genome • marbled crayfish • Marmorkrebs • Procambarus • assembly • clonal • parthenogenesis • evolution

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