Analysis of Alpha-catenin Mediated Intercellular Adhesion in Drosophila

Dynamic linkage between the cadherin-catenin complex (CCC) and the actin cytoskeleton at Adherens Junctions is essential for cell-cell adhesion in epithelial cells. Alpha-catenin is a core component of the CCC that is responsible for maintaining the linkage between the actin cytoskeleton and the CCC. As part of my project, I generated an alpha-Catenin (alpha-Cat) RNAi line that was used to knockdown maternal alpha-Cat in Drosophila embryos. Knockdown of alpha-Cat in the female germline produced embryonic lethality that was characterized by severe defects throughout the embryo which suggests that the maternal contribution of alpha-Cat is indispensable for embryonic development. I also investigated if alpha-catenin function is conserved among metazoans and Dictyostelium discoideum. I generated rescue constructs using mouse, zebrafish, worm and slime mold alpha-catenin proteins and attempted to rescue alpha-Cat1 mutant embryos. The results of my analysis suggest that alpha-catenin function is conserved among metazoans but not between Dictyostelium and metazoans.M.Sc.2018-03-09 00:00:0

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon–gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology