Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing

Abstract

BackgroundHybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown.ResultsHere, using 20 diploid and polyploid Fragaria species, we combine approaches from NGS data analysis and phylogenetics to infer evolutionary origins of polyploid strawberries, taking into account coalescence processes. We generate haplotype sequences for 257 low-copy nuclear markers assembled from Illumina target capture sequence data. We then identify putative hybridization events by analyzing gene tree topologies, and further test predicted hybridizations in a coalescence framework. This approach confirms the allopolyploid ancestry of F. chiloensis and F. virginiana, and provides new allopolyploid ancestry hypotheses for F. iturupensis, F. moschata, and F. orientalis. Evidence of gene flow between diploids F. bucharica and F. vesca is also detected, suggesting that it might be appropriate to consider these groups as conspecifics.ConclusionsThis study is one of the first in which target capture sequencing followed by computational deconvolution of individual haplotypes is used for tracing origins of polyploid taxa. The study also provides new perspectives on the evolutionary history of Fragaria. Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1019-7) contains supplementary material, which is available to authorized users.

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

“…All loci targeted in this study appear to be single‐copy genes in Fragaria and across Rosaceae (Kamneva et al ., ); however, our results show that > 70% of these loci have multiple copies in Lachemilla , Alchemilla , and Aphanes (Table S2; Fig. S11).…”

“…Kamneva et al . () implemented a pipeline to assemble single‐copy nuclear gene haplotypes from sequence capture data, but the presence of multiple gene copies in Lachemilla and relatives (Fig. S11, Table S2) makes this task a nontrivial problem that deserves further exploration.…”

“…Total genomic DNA was isolated from fresh, silica‐dried, or herbarium material using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA) following the manufacturer's protocol, or with a modified 2× CTAB method (Doyle & Doyle, ). We used baits designed for Fragaria that target 257 putatively single‐copy orthologous genes (1419 exons) identified in Rosaceae via a comparison of the apple ( Malus ), peach ( Prunus ), and strawberry ( Fragaria ) genomes (Kamneva et al ., ). Genomic DNAs were sheared by nebulization at 30 psi for 70 s, yielding an average shear size of 500 bp as measured by a Bioanalyzer High‐Sensitivity Chip (Agilent Technologies Inc., Santa Clara, CA, USA).…”

“…Stephens et al ., ; Heyduk et al ., ; Sass et al ., ; Moore et al ., ) and investigate patterns of hybridization (e.g. Grover et al ., ; Crowl et al ., ; Folk et al ., ; García et al ., ; Kamneva et al ., ; Mitchell et al ., ). In this paper, we use a phylogenomic dataset of 396 nuclear loci and complete plastomes assembled via targeted sequence capture to (1) estimate the phylogeny of Lachemilla with a focus on relationships among the major clades, (2) reexamine the source of incongruence between the plastid and nuclear phylogenies using genome‐scale data, and (3) investigate the sources of discordance among gene trees and species trees.…”

Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments

“…vesca as well as the Asian 2 x F. mandshurica (Fig. ; Kamneva et al ., ). Recurrent formation, representing multiple independent origins, has been observed in the 10 x and 8 x taxa (Dillenberger et al ., ).…”