Revolutionizing avocado breeding: Comprehensive genome assembly unlocks secrets of Hass cultivar

Avocado (Persea americana)  is a key species within the Lauraceae family, has seen limited genetic research despite the commercial success of its Hass cultivar. Presently, research has sequenced only a few species within this family, providing insight into plant evolution yet revealing genetic complexities due to ancient lineage sorting. The Hass avocado’s genome assembly remains highly fragmented and incomplete, highlighting the need for improved genetic mapping.

In August 2022, Horticulture Research published a perspective entitled by “A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes”.

Initially, Hass cultivar was sequenced using HiFi reads from PacBio sequencing and assembled to the chromosome level with an average read length of 15 kb, allowing for 47.9× coverage of the expected 920 Mb genome. The genome was assembled using Hifiasm, yielding a 935 Mb genome with an N50 of 26 Mb. Hifiasm was also used to generate haplotig assemblies, and the two sets of haplotigs contained many highly similar regions. Organelle genomes (i.e., mitochondria and plastome) were assembled using the GetOrganelle tool and found that the avocado mitochondrial genome is more than three times the size of the chloroplast genome, which consists of two assemblies of 152732 bp each. In addition, the Hifiasm-assembled contigs were screened to remove organellar genomes, resulting in a 913 Mb assembly. Contigs were then aligned to form pseudochromosomes using SynMap in CoGe, producing 13 pseudomolecules covering about 95% of the predicted avocado genome size. A number of duplications and inversions were identified by self-self syntenic comparisons, and synteny plots revealed two genome-wide duplication events (WGDs). Circos plots were further utilized to re-plotted the syntenic blocks obtained from CoGe and thus observed various large syntenic sections between chromosomes, including a number of macro- and micro-syntenic regions. The self synteny showed a higher number of gene duplications on Chr3 and Chr5 compared to other chromosomes. Repeat analysis showed that 62% of the assembled genome was masked, highlighting the prevalence of repetitive elements. Gene annotation using BRAKER with RNA-Seq data predicted 46,147 genes with a high level of completeness. These genes were predominantly located in non-repeat regions. Furthermore, the research explored primary metabolism in avocado, revealing the production of heptose sugars and the genes regulating their biosynthesis. In terms of fruit ripening, the study found unique aspects of cellulase action in avocado compared to other fruits. Analysis of potassium channels and transporters underscored avocado's rich potassium content. Lastly, orthologous gene analysis across various species highlighted unique gene clusters in avocado, associated with various biological processes and enzyme activities.

In summary, this study on the Hass avocado cultivar has provided a detailed perspective on their genetic structure, function, and evolution. These findings will contribute to the development of elite avocado varieties with improved yields and fruit quality, as well as to a deeper understanding of early angiosperm evolution, particularly within the magnoliid family.

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References

Authors

Onkar Nath, Stephen J. Fletcher, Alice Hayward, Lindsay M. Shaw, Ardashir Kharabian Masouleh, Agnelo Furtado, Robert J. Henry* and Neena Mitter*

Affiliations

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia

About Robert J. Henry & Neena Mitter

Robert J. Henry: He is currently Professor of Agriculture Innovation at the University of Queensland. Professor Henry's area of specialization is the study of crops using molecular tools. He has particular interests in Australian flora and plants of economic and social importance, and has led genome sequencing research to access novel genetic resources and diversify  food crops to provide better food.

Neena Mitter: Prof Neena Mitter is the founding Director of both the QAAFI Centre for Horticultural Science and the Australian Research Council Industrial Transformational Research HUB for Sustainable Crop Protection at The University of Queensland (UQ). As Director of the Center, Neena oversees the Center's three major research themes: 'Horticulture Crop Breeding and Agronomy', 'Plant Protection' and 'Emerging Technologies', and builds careful networks between the Center's multiple regional locations, working closely with industry, growers and government to promote innovation, productivity and economic growth.