Phylogenomic analysis of transcriptome data elucidates co‐occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Abstract

We found that polyploidy and the origin of the Yucca-Agave bimodal karyotype co-occur on the same lineage consistent with the hypothesis that the bimodal karyotype is a consequence of allopolyploidy. We discuss this and alternative mechanisms for the formation of the Yucca-Agave bimodal karyotype. More generally, we illustrate how the use of next-generation sequencing technology is a cost-efficient means for assessing genome evolution in nonmodel species.

A Chloroplast Phylogeny of Agavaceae subfamily Chlorogaloideae: Implications for the Tempo of Evolution on Serpentine Soils

“…It is unclear how a bimodal karyotype arose within Agavaceae. Results by McKain et al (2012) are consistent with allopolyploidy, however the possibility of a fissionfusion event cannot be ruled out. Within this clade, only Hosta, Agave s. l., Yucca, Hesperaloe, and Hesperoyucca have a chromosome number of n = 30 (25S [small] + 5L [large], or some multiple based on ploidy level).…”

“…Notably, all members of Chlorogaloideae have a bimodal karyotype, in which chromosomes fall into two distinct groups of sizes (Sato 1935;Gould 1942;Sherman 1969;Cave 1970;Fernandez and Daviñ a 1991). The discovery of this character first indicated a close relationship to members of Agavaceae, in which the presence of bimodal karyotypes has long been recognized (McKelvey and Sax 1933;Akemine 1935;Sato 1935;Watkins 1936;Granick 1944;Cave 1948Cave , 1970Sen 1975;Tamura 1995;Pires et al 2006;McKain et al 2012).…”

“…However, no member of Chlorogaloideae and only three genera of monocots were included in that study. We also consider the significance of our phylogenetic results for the evolution of the distinctive bimodal karyotype of Agavaceae (McKain et al 2012).…”

Retrotransposon proliferation coincident with the evolution of dioecy inAsparagus

“…Raw sequence reads for A. asparagoides have been deposited under BioProject PRJNA326431. Using a pipeline from McKain et al (2012; https://github.com/ mrmckain/FASTKs), we first identified putative paralogs in each filtered transcriptome assembly using all vs. all blastn (1e-40 cutoff). Peptide sequences for hit pairs longer than 100 amino acids were aligned using MUSCLE (v3.8.31), then codon alignments were inferred using PAL2NAL (v13) (Suyama et al 2006).…”

“…Transcriptome assemblies were generated for two species sampled broadly across the phylogeny: a basal diploid hermaphrodite (A. asparagoides; 2n = 2· = 20), and diploid dioecious garden asparagus (A. officinalis; 2n = 2· = 20). Intraspecific paralog pairs and interspecific orthologous gene pairs were inferred to generate Ks (synonymous substitution rate) distributions, and assess the relative timing of WGD event relative to speciation events (Blanc and Wolfe 2004;Cui et al 2006;McKain et al 2012;Doyle and Egan 2010). Despite being an outlier in terms of genome size, A. asparagoides was utilized for the comparison given that it is a basal member of the genus, shares the same diploid chromosome count as A. officinalis, and that transcriptome-based Ks analyses are independent of genome size.…”