Completion Date
1-2020
Advisor(s)
Jean Davidson
Abstract
Through Baker-Koob funding, we obtained Cal Poly’s first long read sequencer; our subsequent research marked the first use of next generation sequencing at Cal Poly and resulted in the first-ever draft sequence of the B. violaceus genome. Whole genome sequencing for B. violaceus was completed using a dual platform approach, implementing Illumina short read and Nanopore long read sequencing technologies for single read and hybrid assembly pipelines (Fig. 1). Approximately 7.5 Gb of Illumina and 900 Mb of Nanopore data were acquired. Assembly efforts have been broken down into two phases: single read assembly and hybrid assembly. Short reads were deconvoluted using Kraken V2.0.1 and assembled with String Graph Assembler V1.0.0 on Illumina’s cloud compute service (i.e. BaseSpace) to develop the first draft genome for B. violaceus (Fig 2). Using comparative bioinformatics algorithms such as Augustus V3.3.3 and GhostKOALA V2.2.0, we have annotated thousands of putative genes to further unveil the evolutionary origins of colonial ascidians and identify potential gene regulatory networks. BUSCO assessment (V3.0) of this draft estimate 60-80% completion via observation of conserved eukaryotic and metazoan orthologs in putative gene predictions. Furthermore, the Keeling Lab at Cal Poly aims to apply genomic information on B. violaceous to expand available experimental techniques; designing molecular assays will provide empirical insight into the underlying mechanisms of regeneration in colonial ascidians. This genome sequence will play a critical role in the advancement of ascidian stem cell biology and promote the use of an underestimated non-model organism.
URL: https://digitalcommons.calpoly.edu/bkendowments/86
Copyright
This work is licensed under a Creative Commons Attribution 4.0 International License.