Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.)

Abstract

BackgroundRadish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized.ResultsIn this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred.ConclusionComprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.

Weed evolution: Genetic differentiation among wild, weedy, and crop radish

“…F ST analyses clearly cluster weedy and native members of this subspecies together, and while the AMOVA found that weedy and native R. r. raphanistrum are significantly differentiated, they are less differentiated than the weeds are from either the crop R. sativus or the other native subspecies R. r. landra (Table ). This conclusion is in agreement with a previous phylogenetic analysis based on eight transcriptomes, which found that weedy R. r. raphanistrum and native R. r. raphanistrum are sister taxa, and that both are more closely related to the other native Raphanus than to any cultivar (Shen et al., ).…”

“…R. pugioniformis is a little‐studied endemic of the eastern Mediterranean (Ziffer‐Berger, Hanin, Fogel, Mummenhoff, & Barazani, ). The relationships among these species are not well‐resolved (Ziffer‐Berger et al., ), but an analysis of cDNA sequence from one population of each of eight Raphanus taxa (not including R. pugioniformis ) provided strong support for the monophyly of the crop cultivars, as well as monophyly of native and weedy R. r. raphanistrum (Shen et al., ).…”

“…However, since flowering time has only been reported for one native population, and the phylogeny in Shen et al. () was based on only a single population of each Raphanus taxon and did not include R. pugioniformis , neither the origin of weedy radish nor whether the weeds have evolved earlier flowering is clear. We estimated genetic differentiation for flowering time and molecular markers for all named species and subspecies in the genus Raphanus , including a total of 15 populations from all three wild taxa from the native range, eight weedy R. r. raphanistrum populations from outside the native range, and 21 crop cultivars from all four groups (), to address two questions.…”

Mitochondrial Genome Sequencing Reveals orf463a May Induce Male Sterility in NWB Cytoplasm of Radish

“…Regarding the origin of orf463a, we confirmed the presence of this gene in R. raphanistrum and R. maritimus (i.e., wild radish) (Table 4) which are possible ancestors of R. satvius [22,39]. A sequence analysis indicated that the orf463a sequence in R. maritimus contains nine nucleotide substitutions, seven of which are nonsynonymous.…”

Cytokinin-dependent secondary growth determines root biomass in radish (Raphanus sativusL.)

“…Lastly, cross-species comparison with a model species is relatively straightforward due to the evolutionary proximity of radish to Arabidopsis thaliana , whose root development has been studied extensively. Currently, draft radish genome sequence data ( Kitashiba et al , 2014 ) and about 300 000 expressed sequence tags (ESTs) are publicly available ( Shen et al , 2013 ).…”