Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

Abstract

Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

“…While several rearrangements and inversions were detected between ancestral diploid chromosomes, they primarily consisted of large, syntenic blocks with high degrees of collinearity ( Figure 6). These results demonstrate that the structural conservation retained between octoploid species extends to broader Fragaria taxa, including strawberry species that are estimated to have diverged~7.5 million years ago and beyond that to a distantly related Rosaceous species estimated to have diverged 33 M years ago (Njuguna et al, 2013;Qiao et al, 2016). This is unique compared to extensive karyotype evolution documented in polyploid species involving numerous chromosomal fusion and rearrangement events, e.g.…”

“…Large inversions reflect the orientations of genome assemblies, not whole-chromosome inversions. Divergence estimates for F. vesca and F. iinumae, and Fragaria and Rubus are fromQiao et al (2016) and estimate for date of F. × ananassa polyploid are fromNjuguna et al (2013).…”

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

“…In this study, we take advantage of the fact that polyploidy is an important mode of speciation in wild strawberries ( Fragaria L.), a genus that originated around 3–8 million yr ago (Liston et al ., ; Qiao et al ., ) and has 22 extant species with a broad distribution in the northern hemisphere (Staudt, ; Liston et al ., ). While Fragaria has two centers of species diversification (in East Asia and Europe–North America; Liston et al ., ), we focused on diploid and polyploid Fragaria that occur in North America, South America, Europe and Northeast Asia (Fig.…”

Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

“…and South American F. chiloensis (L.) Duchesne ex Weston (Liston, Cronn & Ashman, 2014). Phylogenetic analysis of octoploid Fragaria species have been conducted using nuclear genes (Rousseau-Gueutin et al, 2009;DiMeglio et al, 2014), almost complete chloroplast genomes (Njuguna et al, 2013;Govindarajulu et al, 2015), and genome-wide markers (Tennessen et al, 2014;Govindarajulu et al, 2015;Qiao et al, 2016). These studies support a model in which the octoploid Fragaria genome contains four ancestral sub-genomes.…”