Comparative transcriptomics identifies patterns of selection in roses

Abstract

BackgroundRoses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge.ResultsHere, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basye’s Thornless’ (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes.ConclusionsWe expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1585-x) contains supplementary material, which is available to authorized users.

A genomic link in China roses: and they all lived prickly but water deficient ever after?

“…We detected no significant sequence variation in the means of nonsynonymous (Ka) vs. synonymous (Ks) change between these BT and OB orthologous genes, indicating that likely the regulation of gene expression, not the encoding potential, of these trichome-related genes might underlie the regulation of prickleless in BT. Indeed, we detected five genes featuring at least two-fold significant expression changes in very young shoots including apical meristems between BT and OB ( Figure 5B) (Li et al, 2018). The expression of positive regulators GIS and TTG1 were decreasing, while the negative regulator R3 type MYBs (TRY-and MYBH-like) and one MYB8-like genes increased its expression in BT comparing to OB ( Figure 5B, Supplementary Table S33).…”

“…Determination of a highly heterozygous genome for roses remains challenging, as seen by the very fragmented assembly trials of three species (Lu et al, 2016;Nakamura et al, 2017;Raymond et al, 2018), and currently only two versions of chromosome-level genome sequences for doubled-haploid materials of one cultivated founder genotype (Rosa chinensis 'Old Blush', haploOB) in domestication of modern cultivated roses have been described (Hibrand Saint-Oyant et al, 2018;Raymond et al, 2018). Enormous sequence variation including single-nucleotide-polymorphisms (SNPs), insertion/deletions (indels), inversions and translocations can exist between varieties of rose like in maize and may contribute to key agricultural traits (Li et al, 2019a;Sun et al, 2018;Yang et al, 2019). Therefore, a complete picture of genome assembly for diploid rose genotype is necessary for the purpose of comparative genomics in identifying molecular genetic bases of key morphological traits that have been pursued for decades in roses.…”

“…These have allowed this species frequently used as parental materials for constructing a set of genetic populations aiming at dissecting the genetic bases of these important traits (Crespel et al, 2002;Hibrand Saint-Oyant et al, 2018;Li et al, 2019c;Li et al, 2015;Shupert et al, 2007;Spiller et al, 2011). Despite of the importance in rose genetics and culture, molecular information of BT is limited with only transcriptomic and molecular markers information available (Crespel et al, 2002;Cui et al, 2020;Hibrand Saint-Oyant et al, 2018;Li et al, 2019c;Li et al, 2018;Li et al, 2015;Shupert et al, 2007;Spiller et al, 2011). In this study, we determined the chromosome-level genome sequences of BT.…”

The complete chloroplast genome sequence of a rambler rose, Rosa wichuraiana (Rosaceae)

“…The genotype R. wichuraiana 'Basye's Thornless' (designated as Rw01) conserved at Texas A&M University is especially valuable for its high resistance to black spot and powdery mildew, hardy, and prickleless traits . It has been used as a model species for studying molecular genetic mechanisms underpinning the regulation of continuous flowering and other traits in woody plants (Semeniuk 1971;Shupert et al 2007;Jones 2013;Dong et al 2017;Li et al 2018). In this study, the complete chloroplast genomes of Rw01 and a second R. wichuraiana genotype (Rw02) were assembled, and the phylogenetic position of R. wichuraiana was studied for the first time.…”

Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets

“…Breeders can explore the inherent rules of plant breeding and cultivation according to the expression status of the RNA-seq in different plants or areas [14]. In addition, the domestication of cultivars, evolution relationships, and genome duplications of the plant genome can be identified by the assembled genes and phylogenetic analysis with transcriptome datasets [14][15][16][17]. Thus, given its numerous usages and advantages, RNA-seq has become a routine tool for plant sciences, and the datasets of RNA-seq have been continuously increasing in the last few years.…”