De Novo Transcriptome Assembly and Comparative Analysis of Differentially Expressed Genes in Prunus dulcis Mill. in Response to Freezing Stress

Mousavi, S. A.; Alisoltani, Arghavan; Shiran, Behrouz; Fallahi, Hossein; Ebrahimie, Esmaeil; Imani, Ali; Houshmand, S.

doi:10.1371/journal.pone.0104541

Cited by 58 publications

(41 citation statements)

References 58 publications

(81 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All runs were from either general transcriptome sequencing (Jo et al 2015) or controls of differential expression experiments (Wang et al 2013; Mousavi et al 2014; Sanhueza et al 2015). We then converted the runs into their paired FASTQ files using SRA-toolkit (v. 2.3.4) and quantified expression for each run separately against the peach transcriptome (v. 1.0) using kallisto (Bray et al 2016).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Genomics of Peach and Almond Domestication

Velasco

Hough

Aradhya

et al. 2016

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.

show abstract

Section: Methodsmentioning

confidence: 99%

Evolutionary Genomics of Peach and Almond Domestication

Velasco

Hough

Aradhya

et al. 2016

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…We downloaded ten SRA RNA-seq runs from four peach and almond tissues (Table S2). All runs were from either general transcriptome sequencing (Jo et al, 2015) or controls of differential expression experiments (Wang et al, 2013;Mousavi et al, 2014;Sanhueza et al, 2015). We then converted the runs into their paired FASTQ files using ) and quantified expression for each run separately against the peach transcriptome (v. 1.0) using kallisto (Bray et al, 2016).…”

Section: Gene Expressionmentioning

confidence: 99%

Evolutionary genomics of peach and almond domestication

Velasco

Aradhya

Ross‐Ibarra³

2016

Preprint

View full text Add to dashboard Cite

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated 5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide F ST values support their status as separate species. We estimated a divergence time of 8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.

show abstract

“…RNA-Seq was used to study the response of the reproductive tissues of almond (Prunus dulcis) to frost stress (Mousavi et al, 2014). RNA sequencing resulted in more than 20 million reads from the anther and ovary of almond.…”

Section: Flowermentioning

confidence: 99%