TY - JOUR

T1 - The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

AU - Rendón-Anaya, Martha

AU - Ibarra-Laclette, Enrique

AU - Méndez-Bravo, Alfonso

AU - Lan, Tianying

AU - Zheng, Chunfang

AU - Carretero-Paulet, Lorenzo

AU - Perez-Torres, Claudia Anahí

AU - Chacón-López, Alejandra

AU - Hernandez-Guzmán, Gustavo

AU - Chang, Tien Hao

AU - Farr, Kimberly M.

AU - Brad Barbazuk, W.

AU - Chamala, Srikar

AU - Mutwil, Marek

AU - Shivhare, Devendra

AU - Alvarez-Ponce, David

AU - Mitter, Neena

AU - Hayward, Alice

AU - Fletcher, Stephen

AU - Rozas, Julio

AU - Gracia, Alejandro Sánchez

AU - Kuhn, David

AU - Barrientos-Priego, Alejandro F.

AU - Salojärvi, Jarkko

AU - Librado, Pablo

AU - Sankoff, David

AU - Herrera-Estrella, Alfredo

AU - Albert, Victor A.

AU - Herrera-Estrella, Luis

PY - 2019

Y1 - 2019

N2 - 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. Resequenc-ing 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.

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. Resequenc-ing 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.

KW - Angiosperm phylogeny

KW - Avocado genome

KW - Genome duplications

KW - Genome evolution

KW - Phytophthora

U2 - 10.1073/pnas.1822129116

DO - 10.1073/pnas.1822129116

M3 - Journal article

C2 - 31387975

AN - SCOPUS:85071332309

VL - 116

SP - 17081

EP - 17089

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 34

ER -