Browsing by Author "van der Westhuizen, Hester Christina"

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    Assembly and Annotation of the genome of the sea urchin Tripneustes gratilla
    (Stellenbosch : Stellenbosch University, 2024-12) van der Westhuizen, Hester Christina; Rhode, Clint; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    The sea urchin, Tripneustes gratilla, is considered a culinary delicacy. This species is currently being considered as a candidate for aquaculture in South Africa. Having an annotated genome for T. gratilla will be advantageous for the improvement of commercially important traits. The aim of this study was to assemble and annotate a draft genome for T. gratilla. Four individuals were sequenced - two using Ion Torrent (M1 and F2) and two using Illumina (M10 and U14). The assemblies were created using both de novo and reference-based approaches. The assembly created using the F2 Ion Torrent reads mapped to the M10 Illumina assembly had the best quality overall. Once polished, this genome had a GC content of 35.29%, a total length of 772.9 Mb, and a N50 value of 10 926. BUSCO scores were 46.3% Complete, 0.9% Duplicated, 38.3% Fragmented, and 14.5% Missing BUSCOs. The masked genome was annotated with Braker and after filtering, 33 204 genes were identified. A genome comparison was performed using the annotated genomes of three other sea urchin species: Lytechinus variegatus, Lytechinus pictus, and Strongylocentrotus purpuratus. OrthoFinder and OrthoVenn identified the numbers of orthologues shared by and unique to the four species. These orthologues along with the species tree created with OrthoFinder found that L. pictus, L. variegatus, and S. purpuratus were more closely related to each other than any of them were to T. gratilla and that L. variegatus was the least closely related to T. gratilla. The orthologues were used to run gene enrichment analyses using topGO. OrthoFinder identified the 577 single copy orthologues (SCOs) shared by the species. KaKs Calculator was used to determine the number of SCOs that are under positive selection. Pairwise comparisons detected 10, 8, and 18 SCOs in T. gratilla with L. variegatus, L. pictus, and S. purpuratus respectively that were under positive selection with p<0.05. Five of the genes, COPG2, TBC1D20, FANK1, ASPM, and PAGM were found to overlap between the comparative sets. Four of these genes (TBC1D20, FANK1, ASPM, PAGM) play a role in testes and spermatogenesis and TBC1D20 has been associated with viral activity.