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

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.

Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

“…These are woody clades with relatively high species diversity but low rates of molecular evolution. Other approaches, such as RAD‐seq, have been successful in Viburnum (Eaton et al, 2017 ; Landis et al, 2020 ), and in other woody plant groups, including Quercus (Hipp et al, 2014 ) and Salix (Wagner et al, 2020 ). The major advantage of these probe‐less methods is the enormous number of SNPs that they typically recover.…”

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

“…RAD-seq is being commonly employed to study the intra-and interspecific genomic divergence, to investigate the levels of genomic diversity and to resolve phylogenomic relationships of diverged lineages (Paun et al, 2016;Rochette and Catchen, 2017;Brandrud et al, 2020). However, the use of RAD-seq in non-model polyploid species is still challenging due to difficulties of inferring allele copy numbers (Clevenger et al, 2015;Wagner et al, 2020). Thus, only recently, RAD-seq has started to be used for analyzing population structure of non-model polyploid plant species (Zohren et al, 2016;Brandrud et al, 2017).…”

“…Restriction site-associated DNA sequencing (RAD-seq; Baird et al, 2008) is a popular method to generate NGS data and investigate genetic variation and population structure, especially for species not benefiting from an available suitable reference genome (Rochette and Catchen, 2017). However, only a limited number of RAD-seq studies have been employed to investigate genetic variation in non-model polyploid species (Zohren et al, 2016;Brandrud et al, 2017;Záveská et al, 2019;Wagner et al, 2020;Wang et al, 2021).…”

nPhase: an accurate and contiguous phasing method for polyploids

“…Linking these variants together to establish which variants cooccur on the same strand of DNA is known as haplotyping or phasing. There is increasing interest in phasing genomes for diverse reasons, such as to obtain more accurate reference genomes [3], better study population genomics [4], improve the accuracy of GWAS studies [5], study the effects of compound heterozygosity [6], investigate Allele-Specific Expression patterns [7], gain insight into polyploid evolution [8,9], better understand the mechanisms of heterosis [10], and dissect the origins of hybrid species [11].…”