title: Comparative Transcriptomics of Strawberries (Fragariaspp.) 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 (Fragariaspp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences ofFragariaspeciesde 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 thatFragariaclosed grouped withRubusand theFragariaclade 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 speciesF. ×ananassagenome. 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 inFragariaand the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.
authors.affiliation: School of Agriculture, Yunnan University Kunming, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Qiao
authors.affiliation: College of Horticulture, Shenyang Agricultural University Shenyang, China.
authors.forename: Li
authors.initials: L
authors.lastname: Xue
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Qia
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Sun
authors.affiliation: Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University Shanghai, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhong
authors.affiliation: Department of Biology, East Carolina University, Greenville NC, USA.
authors.forename: Jinling
authors.initials: J
authors.lastname: Huang
authors.affiliation: College of Horticulture, Shenyang Agricultural University Shenyang, China.
authors.forename: Jiajun
authors.initials: J
authors.lastname: Lei
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Ticao
authors.initials: T
authors.lastname: Zhang
keywords: Fragaria; comparative genomics; evolutionary pattern; positive selection; transcriptome