A Phylogenetic Analysis of the Genus Fragaria (Strawberry) Using Intron-Containing Sequence from the ADH-1 Gene

Abstract

The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae.

HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry ( Fragaria×ananassa )

“…Evidence presented here and recently by others [24,26,32] for a significant contribution of F. iinumae to the genome of the cultivated strawberry suggests an urgent need for the development of a suite of genomics resources for this species to complement the resources already available for F. vesca. Fig 1. Bioinformatics pipeline to classify haploSNP markers into subgenomic identity categories.…”

“…In common with Fedorova [19] and Tennessen et al [26], our model specifies the presence of just two copies of the F. vesca-affiliated A subgenome (denoted C in the Fedorova model). We join Rousseau-Gueutin et al [32], DiMeglio et al [24], and Tennessen et al [26] in postulating allelic and subgenomic contributions from F. iinumae, whose now-evident ancestral role was not known to either Fedorova [19], Senanayake and Bringhurst [20], or Bringhurst [21]. Yet our results suggest caution in demarking a coherent F. iinumae subgenome, given that less than 50% of SNP-SNP markers in the b-subgenome display affinity to F. iinumae.…”

“…[23][24][25]. More recently, Tennessen et al [26] employed a combination of targeted DNA capture and next generation sequencing to obtain evidence for a new genome model AvAvBiBiB1B1B2B2 (2Av,2Bi,2B1,2B2), positing a single subgenome (Av) deriving from an F. vesca-like ancestor, a single subgenome (Bi) derived from an F. iinumae-like diploid ancestor, and two subgenomes (B1 and B2) derived from a F. iinumae-like autotetraploid.…”

The aroma volatile repertoire in strawberry fruit: a review

“…The ADH gene was the first protein‐encoding gene completely sequenced in strawberries . This gene and its intron‐containing sequence were commonly applied in ongoing phylogenetic studies on Fragaria species . Until now, limited information about the relationship between ADH transcript expression and volatile performance has been reported in strawberries.…”

Integrated Karyotyping of Woodland Strawberry (<b><i>Fragaria vesca</i></b>) with Oligopaint FISH Probes

“…The knowledge of phylogenetic relationships and the genetic affinities among Fragaria species can help to choose parents from various species for introgression of wild genes into cultivars. However, our current understanding of the relationships between the diploid Fragaria species and the origin of the polyploid species is limited although various analyses have been carried out [Rousseau-Gueutin et al, 2009;Njuguna et al, 2013;DiMeglio et al, 2014;Hirakawa et al, 2014;Liston et al, 2014;Sargent et al, 2016]. …”