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Research article2019Peer reviewedOpen access

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

Rendon-Anaya, Martha; Ibarra-Laclette, Enrique; Mendez-Bravo, Alfonso; Lan, Tianying; Zheng, Chunfang; Carretero-Paulet, Lorenzo; Anahi Perez-Torres, Claudia; Chacon-Lopez, Alejandra; Hernandez-Guzman, Gustavo; Chang, Tien-Hao; Farr, Kimberly M.; Barbazuk, W. Brad; Chamala, Srikar; Mutwil, Marek; Shivhare, Devendra; Alvarez-Ponce, David; Mitter, Neena; Hayward, Alice; Fletcher, Stephen; Rozas, Julio; Sanchez Gracia, Alejandro; Kuhn, David; Barrientos-Priego, Alejandro F.; Salojarvi, Jarkko; Librado, Pablo; Sankoff, David; Herrera-Estrella, Alfredo; Albert, Victor A.; Herrera-Estrella, Luis
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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 similar to 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

avocado genome; angiosperm phylogeny; genome duplications; Phytophthora; genome evolution

Published in

Proceedings of the National Academy of Sciences of the United States of America
2019, Volume: 116, number: 34, pages: 17081-17089 Publisher: NATL ACAD SCIENCES

    Associated SLU-program

    SLU Plant Protection Network

    UKÄ Subject classification

    Agricultural Science
    Evolutionary Biology

    Publication identifier

    DOI: https://doi.org/10.1073/pnas.1822129116

    Permanent link to this page (URI)

    https://res.slu.se/id/publ/101479