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Assembly and annotation of the genome of the sea urchin Tripneustes gratilla
Van der Westhuizen, Hester Christina. 2024. Assembly and annotation of the genome of the sea urchin Tripneustes gratilla. Unpublished masters dissertation. Stellenbosch : Stellenbosch University [online]. Available: https://scholar.sun.ac.za/handle/10019.1/131950 Thesis (MScAgric)--Stellenbosch Uni...
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Stellenbosch : Stellenbosch University
2025
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| access_status_str | Open Access |
| author | Van der Westhuizen, Hester Christina |
| author2 | Rhode, Clint |
| author_browse | Rhode, Clint Van der Westhuizen, Hester Christina |
| author_facet | Rhode, Clint Van der Westhuizen, Hester Christina |
| author_sort | Van der Westhuizen, Hester Christina |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Van der Westhuizen, Hester Christina. 2024. Assembly and annotation of the genome of the sea urchin Tripneustes gratilla. Unpublished masters dissertation. Stellenbosch : Stellenbosch University [online].
Available: https://scholar.sun.ac.za/handle/10019.1/131950
Thesis (MScAgric)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/131950 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:43:10.408Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/131950 Assembly and annotation of the genome of the sea urchin Tripneustes gratilla Van der Westhuizen, Hester Christina Rhode, Clint Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Sea urchins -- Phylogeny Genomes Aquaculture -- Ecology Tripneustes gratilla -- Geographical distribution Sea urchin populations UCTD Van der Westhuizen, Hester Christina. 2024. Assembly and annotation of the genome of the sea urchin Tripneustes gratilla. Unpublished masters dissertation. Stellenbosch : Stellenbosch University [online]. Available: https://scholar.sun.ac.za/handle/10019.1/131950 Thesis (MScAgric)--Stellenbosch University, 2024. ENGLISH ABSTRACT: 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. AFRIKAANSE OPSOMMING: See-pampoentjies, of see-egels soos hulle ook geken word, se gonade/teelkliere is luukse lekkernye wat hoofsaaklik in sushi en sashimi disse gebruik word. In Suid-Afrika word die see- pampoentjie Tripneustes gratilla as ‘n kandidaat vir akwakultuur oorweeg aangesien dit ‘n inheemse spesie is met hoë markaanvaarding. Om ‘n genoom vir hierdie spesie beskikbaar te hê sal voordelig wees vir die verbetering van eienskappe van kommersiële belang. Die doel van hierdie studie was om die eerste konsep genoom te bou en te annoteer vir T. gratilla. Vier see- pampeontjies was gesequence - twee met Ion Torrent (M1 en F2) en twee met Illumina (M10 en U14). Die genoomsamestellings was met de novo en verwysings-gebasseerde metodes geskep en verskillende polerings en maskerings benaderings was uit probeer. Die beste genoomsamestelling op grond van die kwaliteits statistieke was die genoomsamestelling wat geskep was deur die F2 Ion Torrent sekwenseringslees na die gepoleerde M10 Illumina genoomsamestelling te karteer. Hierdie gepoleerde genoom het ‘n GC inhoud van 35.29%, ‘n totale lengte van 772.9 Mb, en ‘n N50 waarde van 10 926 gehad. Die BUSCO tellings was bepaal as 46.3% Volledige, 0.9% Gedupliseerde, 38.3% Gefragmenteerde, en 14.5% Vermisde BUSCO tellings. Die gemaskerde genoom was ook geannoteer. Na filtreting was 33 204 gene vir die genoom geidentifiseer wat vergelykbaar is met dit wat vir ander seepampoentjie spesies gevind word. ‘n Genooms-vlak vergelyking tussen die geannoteerde genoom van T. gratilla en die van drie ander seepampoentjie spesies (L. pictus, L. variegatus, S. purpuratus) was uitgevoer. Die ortholoë en orthogroepe wat uniek was aan elkeen van die spesies en die wat deur die spesies gedeel word was geidentifiseer. Hierdie resultate was gebruik om ‘n spesieboom te trek en die verwantskap tussen die spesies te bepaal. Dit was gevind dat L. pictus, L. variegatus, en S. purpuratus nader aan mekaar verwant was as wat enige van hulle aan T. gratilla was en dat tussen die drie spesies was L. pictus die naaste verwant aan T. gratilla en L. variegatus die minste. Die ortholoë was gebruik vir ‘n geen-verrykings analise en die 577 geidentifiseerde enkelkopie ortholoë (EKO) was gebruik om te bepaal hoeveel van die EKOs onder positiewe seleksie was. Pare-vergelykings het 8, 15, en 18 EKOs in die vergelykende stelle van T. gratilla met L. pictus, L. variegatus, en S. purpuratus onderskeidelik opgespoor wat onder positiewe seleksie was met p < 0.05. Vyf van hierdie gene, naamlik COPG2, TBC1D20, FANK1, ASPM, en PAGM, was gevind in meer as een van die vergelykende stelle. Vier van hierdie gene (TBC1D20, FANK1, ASPM, PAGM) was al voorheen geassosieer met teste/spermatogenese/manlike onvrugbaarheid terwyl TBC1D20 al met virale aktiwiteit geassosieer was. Beide einskappe van belangstelling in akwakultuur. Masters 2025-04-30T12:34:00Z 2025-04-30T12:34:00Z 2024-12 Thesis https://scholar.sun.ac.za/handle/10019.1/131950 Stellenbosch University xxii, xxxix, 169 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Sea urchins -- Phylogeny Genomes Aquaculture -- Ecology Tripneustes gratilla -- Geographical distribution Sea urchin populations UCTD Van der Westhuizen, Hester Christina Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title | Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title_full | Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title_fullStr | Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title_full_unstemmed | Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title_short | Assembly and annotation of the genome of the sea urchin Tripneustes gratilla |
| title_sort | assembly and annotation of the genome of the sea urchin tripneustes gratilla |
| topic | Sea urchins -- Phylogeny Genomes Aquaculture -- Ecology Tripneustes gratilla -- Geographical distribution Sea urchin populations UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/131950 |
| work_keys_str_mv | AT vanderwesthuizenhesterchristina assemblyandannotationofthegenomeoftheseaurchintripneustesgratilla |