Retrotransposon proliferation coincident with the evolution of dioecy inAsparagus

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 = 2· = 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 to 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 (WGD) 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 WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species. KEYWORDS

Practical considerations for plant phylogenomics

“…Transposable element diversity and composition can also be discerned through genome skim data. Although multiple studies have focused on the use of longer read technology such as 454 pyrosequencing (e.g., Harkess et al, 2016), the development of RepeatExplorer (Novák et al, 2013) and Transposome (Staton and Burke, 2015b) enable short reads to be used for transposon identification (e.g., Staton and Burke, 2015a). Using these approaches, genome skim data are able to provide novel insights into the evolution of nuclear genomes, not just organellar genomes.…”

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

“…The hermaphroditic capacity of varietals is believed to be a heritable trait but this trait has yet to be mapped to any genomic coordinates. Sex chromosomes in flowering plants usually evolve from autosomes (Harkess et al 2016; Harkess et al 2017). Likewise, modern monoecious hemp varietals tend to decay into dioecious varietals with inbreeding but little is known about their chromosomal structures (Clarke 2017).…”

Surprising amount of stasis in repetitive genome content across the Brassicales

“…The abundances of TEs in genomes have also been shown to be informative when inferring phylogenetic relationships among taxa, especially in groups rife with polyploidy, such as those in the Brassicales, because it adds an analysis complementary to species tree phylogenies (Dodsworth et al 2015;Harkess et al 2016;Dodsworth et al 2017;Vitales et al 2020). Several studies have used maximum parsimony methods to reconstruct phylogenetic trees, treating TE abundances as continuous characters (Dodsworth et al 2015;Dodsworth et al 2017).…”

“…More recently, a study has shown the power of combining TE sequence similarity with TE abundance to understand evolutionary relationships (Vitales et al 2020). Generally, Copia and Gypsy are the most informative elements due to their high abundance in the genomes, whereas low-abundant TEs are insufficient to resolve the phylogenetic relations with these approaches (Dodsworth et al 2015;Harkess et al 2016;Dodsworth et al 2017;Vitales et al 2020).…”