Department of Genetics, Stellenbosch University, Private bag X1, Matieland 7602, South Africa.
Department of Genetics, Stellenbosch University, Private bag X1, Matieland 7602, South Africa; Mkwawa University College of Education, University of Dar es Salaam, P.O. BOX 2513, Iringa, Tanzania.
Mar Genomics. 2023 Aug;70:101044. doi: 10.1016/j.margen.2023.101044. Epub 2023 May 15.
Haliotis midae or "perlemoen" is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in minimising the pressure on the wild populations. Here, the draft genome of H. midae has been sequenced, assembled, and annotated. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238 Mb, scaffold N50 of 0. 238 Mb and GC level of 40%. Gene annotation, combining ab initio and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (H. laevigata, H. rubra, H. discus hannai and H. rufescens) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that H. midae is closely related to the Australian Greenlip (H. laevigata) and Blacklip (H. rubra). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.
鲍螺（Haliotis midae 或“perlemoen”）是南非特有的五种鲍鱼物种之一，因其味道鲜美，是唯一具有国际高需求的商业上重要的鲍鱼物种。由于捕捞渔业和偷猎的过度开发，这种鲍鱼物种的高需求导致其野生种群数量减少。促进鲍螺的水产养殖生产应有助于减轻对野生种群的压力。在此，我们对鲍螺的基因组草案进行了测序、组装和注释。该草案组装得到了总长 1.5 Gb、N50 为 0.238 Mb 的 contig、N50 为 0.238 Mb 的 scaffolds 和 40%的 GC 水平。结合从头预测和基于证据的方法进行基因注释，鉴定出了 52,280 个具有蛋白质编码潜力的基因。这些基因被用于预测其他四种鲍鱼（H. laevigata、H. rubra、H. discus hannai 和 H. rufescens）之间共享的同源基因，共有 4702 个同源基因在这五个物种中共享。在鲍鱼的同源基因中，进一步分析了单拷贝基因的选择特征，发现几个参与发育功能的分子调节蛋白在特定的鲍鱼谱系中受到正选择。此外，还进行了基于全基因组 SNP 的系统发育基因组评估，以确认考虑的具有基因组草案的鲍鱼物种之间的进化关系，再次证实鲍螺与澳大利亚绿唇鲍（H. laevigata）和黑唇鲍（H. rubra）关系密切。该研究有助于了解与各种生物系统相关的基因，强调了鲍鱼的进化和发展，为商业种群的遗传改良提供了潜在的应用。
