INSIGHTS INTO THE GENETIC DIVERSITY OF ASIMINA TRILOBA: A STUDY USING GENOME ASSEMBLY AND POPULATION GENETICS

• Main Author: FRIEL, JAMES
• Other Authors: tutor: Martin Kater, A. Bombarely; supervisor: S. Masiero, D. Haak, I. Hormaza, J. Friel, KATER, MARTIN, MASIERO, SIMONA
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Università degli Studi di Milano 2023
• Subjects: Asimina triloba; Pawpaw; Genome assembly; Genotype-by-sequencing; Genetic diversity; Population genetics; Settore BIO/18 - Genetica; Ice Sheet
• Online Access: https://hdl.handle.net/2434/969220

The objective of this PhD thesis was to understand the factors influencing the evolutionary history and distribution of genetic variation in the species Asimina triloba, commonly known as pawpaw. To achieve this, we have produced a high-quality reference genome by assembling a draft genome using PacBio's Sequel II long reads and polishing with Illumina short reads. We first used a genotype-by-sequencing (GBS) to genotype 124 individuals from 28 sites across the state of Virginia to produce a set of single nucleotide polymorphisms (SNPs). We then analysed the population structure and genetic diversity, revealing evidence of isolation by distance and an increase in geneflow over long distance by individuals along rivers. Following on from this, an improved genome assembly was produced by incorporating HiFi, Hi-C, and RNA-seq data, resulting in an annotated, highly contiguous, and accurate genome assembly. The improved draft assembly provided a more comprehensive view of the genome structure and organization of A. triloba, allowing for the construction of pseudochromosomes and genome annotation, including the identification of repeat and transposable elements. An additional population genetics study was then carried out using the same GBS approach to analyse over 300 wild individuals collected from across North America. Our analysis provided insight into the overall diversity of the species and indicated that A. triloba may have experienced a bottleneck. This may have resulted from a reduced population size in its Pliocene refugia prior to the species’ northern migration after the retreat of the Laurentide Ice Sheet. This research has important implications for understanding the mechanisms underlying genetic diversity in the species and conservation efforts.