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Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus

View ORCID ProfileAlex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna, Jim Leebens-Mack
doi: https://doi.org/10.1101/048462
Alex Harkess
1Department of Plant Biology, University of Georgia, Athens GA, USA
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Francesco Mercati
2Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy
3Institute of Biosciences and BioResources, Division of Palermo, National Research Council, 900129 Palermo, Italy
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Loredana Abbate
3Institute of Biosciences and BioResources, Division of Palermo, National Research Council, 900129 Palermo, Italy
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Michael McKain
4Donald Danforth Plant Science Center, St. Louis, MO, USA
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J. Chris Pires
5Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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Tea Sala
6Consiglio per la Ricerca in Agricoltura e l’analisi dell'economia agraria (CREA), Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
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Francesco Sunseri
2Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy
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Agostino Falavigna
6Consiglio per la Ricerca in Agricoltura e l’analisi dell'economia agraria (CREA), Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
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Jim Leebens-Mack
1Department of Plant Biology, University of Georgia, Athens GA, USA
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Abstract

Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements in particular have undergone a marked proliferation in dioecious species. In the absence of a detectable whole genome duplication event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.

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  • ↵* Corresponding author

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Posted April 13, 2016.
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Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus
Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna, Jim Leebens-Mack
bioRxiv 048462; doi: https://doi.org/10.1101/048462
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Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus
Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna, Jim Leebens-Mack
bioRxiv 048462; doi: https://doi.org/10.1101/048462

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