Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data.

Natascha D. Wagner,Elvira Hörandl,Li He

doi:10.3389/fpls.2020.01077

Natascha D. Wagner, Elvira Hörandl + Show 1 more

Open Access

https://doi.org/10.3389/fpls.2020.01077

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Abstract

Polyploidy is common in the genus Salix. However, little is known about the origin, parentage and genomic composition of polyploid species because of a lack of suitable molecular markers and analysis tools. We established a phylogenomic framework including species of all described sections of Eurasian shrub willows. We analyzed the genomic composition of seven polyploid willow species in comparison to putative diploid parental species to draw conclusions on their origin and the effects of backcrossing and post-origin evolution. We applied recently developed programs like SNAPP, HyDe, and SNiPloid to establish a bioinformatic pipeline for unravelling the complexity of polyploid genomes. RAD sequencing revealed 23,393 loci and 320,010 high quality SNPs for the analysis of relationships of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix). Polyploid willow species appear to be predominantly of allopolyploid origin. More ancient allopolyploidization events were observed for two hexaploid and one octoploid species, while our data suggested a more recent allopolyploid origin for the included tetraploids and identified putative parental taxa. SNiPloid analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. Our RAD sequencing data demonstrate that willow genomes are shaped by ancient and recent reticulate evolution, polyploidization, and post-origin divergence of species.

Highlights

The impact of polyploidy in plant evolution is evident (Soltis and Soltis, 2009; Wood et al, 2009; Jiao et al, 2011; Mayrose et al, 2011; Barker et al, 2016), there is much to discover about the impact of polyploidy on evolution of plant genomes
To test for an influence of reticulate evolution on the genetic composition of the included species, we explored the genetic structure of each sample
Reduced representation libraries like Restriction Associated DNA (RAD) sequencing are frequently used to analyze intraspecific population structure, closely related species groups and to infer phylogenetic relationships of diverged lineages based on high numbers of SNPs (e.g. Cariou et al, 2013; Andrews et al, 2016; Eaton et al, 2017)

Summary

Introduction

The impact of polyploidy in plant evolution is evident (Soltis and Soltis, 2009; Wood et al, 2009; Jiao et al, 2011; Mayrose et al, 2011; Barker et al, 2016), there is much to discover about the impact of polyploidy on evolution of plant genomes. Polyploids may originate from combining genomes via hybridization (allopolyploids) or from intraspecific genome duplication (autopolyploids). Post-origin evolution and introgression may further leave genomic signatures (Peralta et al, 2013). This information, is crucial to understand the evolution of species. The potential offered by the rise of high-throughput sequencing tools to analyze the origin of natural polyploid plant species has not yet been fully exploited. The main reasons might be the difficulties in variant calling, especially the need to distinguish different alleles derived from the same parent

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