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Title: The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation
Authors: Rendón-Anaya, Martha
Ibarra-Laclette, Enrique
Méndez-Bravo, Alfonso
Lan, Tianying
Zheng, Chunfang
Carretero-Paulet, Lorenzo
Perez-Torres, Claudia Anahí
Chacón-López, Alejandra
Hernandez-Guzmán, 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
Sánchez Gracia, Alejandro
Kuhn, David
Barrientos-Priego, Alejandro F
Salojärvi, Jarkko
Librado, Pablo
Sankoff, David
Herrera-Estrella, Alfredo
Albert, Victor A
Herrera-Estrella, Luis
Keywords: Science::Biological sciences
Issue Date: 2019
Source: Rendón-Anaya, M., Ibarra-Laclette, E., Méndez-Bravo, A., Lan, T., Zheng, C., Carretero-Paulet, L., Perez-Torres, C. A., Chacón-López, A., Hernandez-Guzmán, G., Chang, T., Farr, K. M., Barbazuk, W. B., Chamala, S., Mutwil, M., Shivhare, D., Alvarez-Ponce, D., Mitter, N., Hayward, A., Fletcher, S., ...Herrera-Estrella, L. (2019). The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proceedings of the National Academy of Sciences, 116(34), 17081-17089.
Journal: Proceedings of the National Academy of Sciences 
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.
ISSN: 0027-8424
DOI: 10.1073/pnas.1822129116
Schools: School of Biological Sciences 
Rights: © 2019 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercialNoDerivatives License 4.0 (CC BY-NC-ND).
Fulltext Permission: open
Fulltext Availability: With Fulltext
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