The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

Abstract

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species.

Keywords: Phytophthora; angiosperm phylogeny; avocado genome; genome duplications; genome evolution.

Fig. 1.

Population genomic structure of avocado. (A) Principal component analysis (PCA) of genome-wide SNPs reveals population groupings among races and varieties. The Guatemalan and West Indian/Costa Rican accessions are closely related, while the Mexican (P. americana var. drymifolia) specimens are more diverse, with the unusual individual Tiny Charly drawn toward the outgroup species P. schiedeana by PC2. Hass and its sport Mendez are tightly clustered and intermediate between Mexican and Guatemalan and West Indian/Costa Rican on PC2. (B) NGSAdmix analysis reveals similar population structure at K = 3. The P. schiedeana outgroup is distinct, and the Hass reference genome is revealed to be admixed between Guatemalan–West Indian and Mexican source populations, the Mexican source clearly contributing greater than 50%.

Fig. 2.

SNP diversity analysis reveals the hybrid genomic background of Hass avocado. (A) Twenty-two megabases (Mb) of anchored DNA on chromosome 4 exemplify the hybrid nature of Hass, in which genomic introgression from the Guatemalan avocado race (var. guatemalensis) occurred into a Mexican (var. drymifolia) genetic background. (B) While in the top chromosome arm the blue trend line shows a low differentiation index (F_ST) between Hass and the Mexican subpopulation as well as a high introgression signal $\left({\widehat{f}}_d\right)$ from var. drymifolia into Hass, these signals should not be misinterpreted as introgression events, since the absolute genetic divergence $\left(d_{XY}\right)$ between both sets of accessions does not vary along the chromosome. The lower arm of the chromosome, however, has inverted trends, where our estimators describe an elevated introgression signal from var. guatemalensis into Hass, as confirmed by the decay in $d_{XY}$ (red trend line), and higher F_ST between Hass and Mexican accessions. (C) No evidence for selective sweeps or domestication signatures were identified; Mexican and Guatemalan subpopulations displayed neutral D values while Hass maintained extreme D values at the theoretical upper limit of the estimator (∼2). Such positive values reflect a “bottlenecked” origin with clonal expansion after the very recent foundation of the cultivar only a few decades ago. Each dot in the plots corresponds to statistics for SNP data in nonoverlapping 100-kb windows (confidence interval of 0.90 for graphical smoothed conditional means). Apparent centromeric regions are located at around 10 Mb, where F_ST, ${\widehat{f}}_d$ and $d_{XY}$ intersect and Tajima’s D for Hass decreases.

Fig. 3.

Phylogenomic and whole-genome duplication history of avocado. (A) An ultrametric time tree based on universally present single-copy protein sequences depicts 1 of 3 common resolutions of Persea (Magnoliidae) relationships to other flowering plants. This topology, showing avocado sister to monocots plus eudicots, mirrors phylogenetic relationships derived from syntenic distances. Here, the split time between the last common ancestor of avocado and the monocot/eudicot crown group is less than 4 million y. Pie charts at 50% positions on branches show proportions of gene gains (orange) versus losses (blue) as determined by BadiRate’s birth–death–innovation model. Yellow–green (greater–lesser) heat map to the right of the tree depicts relative numbers of genes in the modern genomes. Syntenic analysis revealed 2 independent WGD events (red stars) during avocado’s evolutionary history. (B) Hass avocado (bottom 4 genomic blocks) shows 4:1 intercalated syntenic relationships with Amborella (upper block). (C) Syntenic homologs in avocado show a bimodal K_s distribution suggestive of 2 polyploidy events (numbered 1 and 2; cyan: Hass:Hass paralogs; green: Hass:drymifolia homologs) following the split between magnoliids and Amborella (red syntenic homologs). These events postdate the species split between Vitis and avocado (purple syntenic homologs) and so are independent of the gamma triplication that underlies Vitis.