Biology subjects

Arpaia, M. L.

Publications and source records attributed to Arpaia, M. L..

3 recordsLinked to original sources

bioRxiv2026

Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci

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. Avocado genomes have so far come from type A cultivars. 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 Omni-C data, the assembly places 859.8 Mb, 96% of the expected 896 Mb genome, in 12 chromosomes with an NG50 of 84.5 Mb, a consensus quality of QV 69.95, and 97.3% complete BUSCO genes; repeats occupy 64.0% of the assembly, and 35,386 protein-coding genes were predicted. We compared Thille with the type A cultivars Hass and Puebla, a predominantly Guatemalan hybrid, and with a West Indian (WI) accession, a Lowland botanical group variety of unreported flowering type. The assemblies differ by large rearrangements, including an 18.8 Mb inversion on chromosome 12 specific to Hass. Using phased reads and haplotype assemblies, we reconstructed the alleles of candidate flowering genes from a type A versus type B Fst scan. Both WI haplotypes carry the recessive SDMYB allele found in Thille; based on this study and the previous study of SDMYB, we predict the WI accession to be type B. Six genes, including SDMYB, carry an allele shared by all three type A cultivars and absent from Thille and WI. The genome and HiFi reads are available under BioProject PRJNA1142556.

genomics↗

bioRxiv2025

Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado

In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flowers in the morning and male-phase flowers in the afternoon, while B-types show the complementary pattern, a form of heterodichogamy. We map this dimorphism in avocado to a genomic region overlapping a single strong candidate gene, SDMYB, where a dominant haplotype confers A-type flowering. SDMYB belongs to a subgroup of R2R3 MYB transcription factors established as key regulators of floral maturation in diverse species with links to circadian jasmonate signaling. Haplotypes at this locus form an ancient trans-species polymorphism maintained by negative frequency-dependent balancing selection over 44 million years, and they segregate in at least 26 non-avocado species, including in a genus where this mating system has not been reported. Across several species examined, rhythmic diel SDMYB expression is associated with biphasic floral anthesis, and the dominant allele, which contains nonsynonymous changes in conserved functional domains, exhibits a cis-regulated phase delay, corresponding to the delayed 2nd anthesis of A-types. The coupling of dichogamy with diel flower movements, widespread among magnoliids, is a likely precursor to daily forms of heterodichogamy. Absence of the SDMYB polymorphism in true cinnamon, which exhibits a highly similar mating system, suggests the possibility that heterodichogamy has convergently evolved within Lauraceae.

evolutionary biology↗

bioRxiv2022

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

O_LIThe domestication history of avocado (Persea americana) remains unclear, in part due to a lack of suitable genomic tools. C_LIO_LIWe created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. We also compiled a database of 34 resequenced accessions that represented the three botanical races of P. americana. C_LIO_LIOur genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91% and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate the population genomics of avocado. Our analyses were consistent with three separate domestication events; we estimated that the Mexican race diverged from the Lowland (formerly known as West Indian) and Guatemalan races >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan race, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types. C_LIO_LIWith the help of a new reference genome, we inferred the domestication history of avocado and identified genes that may contribute to heterodichogamy, including genes with functions in pollination and floral development. C_LI

genomics↗