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Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17081-17089. doi: 10.1073/pnas.1822129116. Epub 2019 Aug 6.

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

Author information

1
Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.
2
Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
3
Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.
4
Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia, México.
5
Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.
6
Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
7
Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent, Belgium.
8
Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato, México.
9
División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato, México.
10
Department of Biology, University of Florida, Gainesville, FL 32611.
11
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.
12
School of Biological Sciences, Nanyang Technological University, Singapore 637551.
13
Department of Biology, University of Nevada, Reno, NV 89557.
14
Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
15
Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.
16
Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.
17
Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami, FL 33158.
18
Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco, México.
19
Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen, Denmark.
20
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse, France.
21
Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260; vaalbert@buffalo.edu lherrerae@cinvestav.mx.
22
Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México; vaalbert@buffalo.edu lherrerae@cinvestav.mx.
23
Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409.

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.

KEYWORDS:

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

PMID:
31387975
DOI:
10.1073/pnas.1822129116
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