RT Journal Article
SR Electronic
T1 The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen-Influenced Gene Space Adaptation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 654285
DO 10.1101/654285
A1 Martha Rendón-Anaya
A1 Enrique Ibarra-Laclette
A1 Alfonso Méndez Bravo
A1 Tianying Lan
A1 Chunfang Zheng
A1 Lorenzo Carretero-Paulet
A1 Claudia Anahí Perez-Torres
A1 Alejandra Chacón-López
A1 Gustavo Hernandez-Guzmán
A1 Tien-Hao Chang
A1 Kimberly M. Farr
A1 W. Brad Barbazuk
A1 Srikar Chamala
A1 Marek Mutwil
A1 Devendra Shivhare
A1 David Alvarez-Ponce
A1 Neena Mitter
A1 Alice Hayward
A1 Stephen Fletcher
A1 Julio Rozas
A1 Alejandro Sánchez Gracia
A1 David Kuhn
A1 Alejandro F. Barrientos-Priego
A1 Jarkko Salojärvi
A1 Pablo Librado
A1 David Sankoff
A1 Alfredo Herrera-Estrella
A1 Victor A. Albert
A1 Luis Herrera-Estrella
YR 2019
UL http://biorxiv.org/content/early/2019/06/17/654285.abstract
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.