Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci
Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Avocado (Persea americana Mill.) is heterodichogamous: each flower opens first as female and then as male, and cultivars fall into two complementary flowering types, A and B, determined by the transcription factor SDMYB, whose dominant allele confers type A. Published avocado genomes come from type A cultivars or from accessions of unreported flowering type. Here we report a chromosome-level genome of Thille, a type B cultivar used in breeding. From 72.2 Gb of PacBio HiFi reads (81x coverage) and Dovetail Omni-C data, the assembly places 885.4 Mb, 98.8% of the expected 896 Mb genome, in 12 chromosomes with an NG50 of 84.5 Mb, a consensus quality of QV 70.02, and 99.7% complete BUSCO genes; repeats occupy 64.0% of the assembly, and 36,349 protein-coding genes were predicted. We compared Thille with the type A cultivars Hass and Puebla, a Guatemalan x Mexican hybrid, and with Unnamed Lowland, an accession of the Lowland botanical group (formerly West Indian) of unreported flowering type. The assemblies differ by large rearrangements, including a 22.6 Mb inversion on chromosome 12 specific to Hass which is most likely due to scaffolding error. Using phased reads and haplotype assemblies, we revisited and reconstructed the alleles of candidate flowering genes from the type A versus type B Fst scan from our previous work. Both Unnamed Lowland haplotypes carry the recessive SDMYB allele found in Thille; based on this study and the previous study of SDMYB, we predict Unnamed Lowland to be type B. We also observe five other genes at which two type A cultivars (Puebla and Gwen) share an allele absent from Thille and Unnamed Lowland, a pattern that requires further investigation. The genome and HiFi reads have been submitted to NCBI under BioProject PRJNA1142556.
Summary
The avocado (Persea americana) is known for its synchronous dichogamous flowering system, in which cultivars are classified as Type A or Type B based on when their female and male reproductive organs mature, a timing offset that encourages cross-pollination (Stout, 1927; Davenport, 1986). While the Type A genome has been extensively studied, primarily through the widely cultivated Hass variety, this study presents the first nearly complete genome of a documented Type B avocado, derived from the Thille variety. Due to Type B being homozygous recessive (Groh et al., 2026), a Type B assembly carries only the recessive allele at the flowering-type locus. Assembling this genotype therefore avoids the allelic heterozygosity expected at that locus in Type A individuals, where the dominant and recessive haplotypes must either be phased or risk collapsing into a single consensus sequence, and it provides an unambiguous reference for the recessive haplotype. The assembly reaches 98.8% completeness, with the 12 largest scaffolds approximating pseudomolecule length and an NG50 of 84.5 Mb. Our analysis reveals structural variants, including inversions and deletions, between the Thille and Hass genomes, particularly on chromosome 10, which houses key flowering markers. This genome and its HiFi sequencing data enrich the genomic resources available for avocado, supporting breeding and further research into this agriculturally significant and resource-intensive crop (Solares et al., 2023).
