PT  - JOURNAL ARTICLE
AU  - Martha Rendón-Anaya
AU  - Enrique Ibarra-Laclette
AU  - Alfonso Méndez Bravo
AU  - Tianying Lan
AU  - Chunfang Zheng
AU  - Lorenzo Carretero-Paulet
AU  - Claudia Anahí Perez-Torres
AU  - Alejandra Chacón-López
AU  - Gustavo Hernandez-Guzmán
AU  - Tien-Hao Chang
AU  - Kimberly M. Farr
AU  - W. Brad Barbazuk
AU  - Srikar Chamala
AU  - Marek Mutwil
AU  - Devendra Shivhare
AU  - David Alvarez-Ponce
AU  - Neena Mitter
AU  - Alice Hayward
AU  - Stephen Fletcher
AU  - Julio Rozas
AU  - Alejandro Sánchez Gracia
AU  - David Kuhn
AU  - Alejandro F. Barrientos-Priego
AU  - Jarkko Salojärvi
AU  - Pablo Librado
AU  - David Sankoff
AU  - Alfredo Herrera-Estrella
AU  - Victor A. Albert
AU  - Luis Herrera-Estrella
TI  - The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen-Influenced Gene Space Adaptation
AID  - 10.1101/654285
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 654285
4099  - http://biorxiv.org/content/early/2019/06/17/654285.short
4100  - http://biorxiv.org/content/early/2019/06/17/654285.full
AB  - 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 two 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.SIGNIFICANCE STATEMENT Avocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocado’s more recent genomic evolutionary history.