PAG Australia 2024

This research provides a comprehensive exploration of the banana pangenome, aiming to enhance sustainability and resilience by supporting breeding against diseases like Fusarium wilt and Black Sigatoka. Using KeyGene’s expertise in generating long-read data in combination with our data science capabilities, we reveal an extensive perspective on banana genetic diversity. Our unique approach leverages the untapped genetic diversity in the wild, initiated through a strategic alliance with Yelloway, the banana breeding company. Using long and highly accurate duplex data, Pore-C, and reference-based scaffolding, we report on the generation of phased Telomere-to-Telomere reference genomes of ten diploid accessions, representing four subspecies. In addition, we generated draft reference genomes of another 50 accessions with a selection refined to near-complete phased genomes using Dorado error correction. Combined with publicly available reference genomes, this now harnesses for the first time an extensive banana pangenome, enriching our understanding of genomic diversity for banana accessions. Our advanced data science capabilities and KeyPan tools facilitated genome comparison within these accessions, enabling identification of genomic loci for disease resistance and other desirable characteristics. This milestone in banana breeding, along with our refined variation calling methods, serves as a crucial resource for marker development, gene discovery, and data visualization using CropPedia®. We anticipate that these technologies and our integrative approach will drive a paradigm shift in banana breeding, bringing a future with more resilient and sustainable banana cultivars.

Most genotyping in agriculture is currently done using SNP arrays. However the cost of arrays based genotypes has not significantly decreased in over a decade. Sequence based genotyping is gaining increased interest due to the decreasing cost of sequence data, as the increased scalability possible. Here we outline the benefits of using nanopore based sequencing for genotyping, for academic and commercial purposes.

Eucalyptus trees are widespread across Australia, providing habitat to a rich biodiversity of marsupials, birds and insects, being key foundation species in natural ecosystems. Using long-read sequencing, we investigated how Eucalyptus genome architecture has changed over time to unveil their adaption to the environment. Firstly, we assembled the genomes of 33 diverse Eucalyptus species, which span millions of years of evolution. We observed a dramatic increase in genome structural variations (SVs) as species diverged, suggesting these play a key role in early architectural divergence. Further divergence led to mutations obscuring rearrangements and a loss of syntenic regions (gene order conservation). Insertions, deletions, duplications, inversions and translocations were observed as major contributors to genome structural divergence. Secondly, we investigated a key species further, E. viminalis, which is experiencing high mortality and dieback in NSW. Long-read sequencing of 50 wild E. viminalis trees across three populations identified thousands of SVs segregating within the populations, potentially influencing adaptation. These SVs had influenced genes in multiple ways, including deleting gene exons, disrupting gene order, translocation of genes, and complete deletion of genes. This included phenotypically important genes such as the terpene synthase gene family. Our pioneering research on SVs in Eucalyptus provides insights into understanding their role in genome evolution and adaptive traits for this ecologically important genus.