Ostrea chilensis Genomic Analysis and Population Diversity: Widespread-Hemizygosity Genomics

This thesis presents a comprehensive study of the genomic architecture and population genetics of Ostrea chilensis, a species of significant ecological, cultural, and economic importance in Aotearoa New Zealand. Through an integrative approach combining third-generation sequencing technologies and novel bioinformatics tools, the research aimed to construct the first annotated reference genome and transcriptome drafts of O. chilensis and to assess the levels of diversity of the populations of Foveaux Strait, Manukau Harbour, and the Chatham Islands.

The first goal of the study was the development of a high-quality de novo whole genome sequence assembly for O. chilensis, employing third-generation sequencing technologies. This resulted in a genome assembly of 1.3 Gb with ten chromosome-level scaffolds, 290 hemizygous region candidates and a circularised complete mitochondrial genome of 16.4 kb, providing a foundational resource for future genetic studies. A transcriptomic analysis revealed 39,351 genes, each with 2.9 isoforms on average, with a significant presence of alternative splicing and tissue-specific expression patterns. A saturation curve of predicted genes shows that an asymptote was reached, indicating a good representation of the total genes of O. chilensis. This highlighted the complexity of the O. chilensis genome and transcriptome, particularly in terms of repetitive elements (59% of the genome) and hemizygous regions, which are known to be associated with adaptability response and immune regulation.

The population genetic analysis of O. chilensis samples from Foveaux Strait, Manukau Harbour, and the Chatham Islands revealed genetically isolated and distinct haplotypes and mitotypes among these sites. This analysis also identified a set of genes consistent with a pattern of variation associated with non-neutral selection. These genes are known to be involved in osmoregulation, immune response, and environmental adaptability. The findings of this study provided new insights into the evolutionary history and divergence of O. chilensis populations. Specifically, a dated time tree, based on the full mitochondrial genome, that characterises the split between the three New Zealand populations analysed and the Chilean populations, and evidence of within- and between-population variation with potential implications on stress resistance, highlighted the importance of population level management for conserving the genetic diversity of this species.

The thesis explored the impact of widespread hemizygosity, reaffirming the potential of hemizygous regions to contribute to genetic potential and adaptability. The findings underscored the necessity of including these regions in genomic analyses when informing selective breeding programmes, contrasting this against a method to exclude them to reduce their noise, suggesting that this latter approach may lead to a loss of diversity in these regions. Additionally, the research highlighted the role of transposable elements in isoform formation and alternative splicing, suggesting their involvement in adaptation.

Methodological improvements to bioinformatic pipelines were an additional outcome of this research. A robust methodology for genome assembly and annotation was developed, including a novel “Pipeline for HiFi/Hi-C Assembly Sequence Elucidation” (PHASE), a “Unified Relative Index of Quality of Assembly” (uRIQA), and an “Isoform-Sequencing Annotation” (ISA) command line tool. The research also addressed the challenges of bioinformatic tool sustainability and accessibility, proposing solutions for long-term usability and management of genomic data called “Platform for Omics on the Web” (POW).

Overall, this thesis provides valuable genomic resources and insights into the patterns of genetic variation of O. chilensis. It also contributes to the broader understanding of mollusc genomics, particularly in the context of hemizygosity and transposable element dynamics. The methodological innovations presented here have broader applicability in the field of genomics for enhancing the efficiency and accuracy of genome assembly and annotation of non-model organisms.