+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

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



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



Bmc Genomics 14: 721



Radish (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. In 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. Comprehensive 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.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 052269773

Download citation: RISBibTeXText

PMID: 24144082

DOI: 10.1186/1471-2164-14-721


Related references

Identification and characterization of microsatellite markers derived from expressed sequence tags (ESTs) of radish (Raphanus satvius L.). Molecular Ecology Notes 7(3): 503-506, 2007

Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence. Breeding Science 58(1): 15-22, 2008

Generation of 919 expressed sequence tags from immature flower buds and gene expression analysis using expressed sequence tags in the model plant Lotus japonicus. Genes & Genetic Systems 77(4): 277-282, 2002

Comprehensive expressed sequence tags analysis during retinal regeneration process. IOVS 42(4): S752, March 15, 2001

In silico identification of miRNAs and their targets from the expressed sequence tags of Raphanus sativus. Bioinformation 8(2): 98-103, 2012

The wild radish from the sea-coast of Japan in connection with the problem of origin of the cultivated forms belonging to the genus Raphanus. Bull. Appl. Bot. Genet. and Plant-Breed, 26: 2, 3-58, 1931

Expressed sequence tags of radish flower buds and characterization of a CONSTANS LIKE 1 gene. Molecules and Cells 8(4): 452-458, 1998

Phylogenetic analysis of cultivated radish (Raphanus sativus L.) germplasm with AFLP. Scientia Agricultura Sinica 38(5): 1017-1023, 2005

Construction of a cDNA library of the Chinese wild Vitis amurensis under cold stress and analysis of potential hardiness-related expressed sequence tags. Genetics and Molecular Research 12(2): 1182-1193, 2013

Comprehensive analysis of expressed sequence tags from the pulp of the red mutant 'Cara Cara' navel orange (Citrus sinensis Osbeck). Journal of Integrative Plant Biology 52(10): 856-867, 2011

Performance of turnip (Raphanus sativus L.) and wild radish (Raphanus raphanistrum L.) as green manure. Pesquisa Agropecuaria Tropical 37(1): 60-63, 2007

Inter- and intraspecific sequence variations of the chloroplast genome in wild and cultivated Raphanus. Plant Breeding 128(2): 172-177, 2009

Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). Dna Research 19(2): 165-177, 2012

Generation of expressed sequence tags (ESTs) for gene discovery and marker development in cultivated peanut. Crop Science 45(1): 346-353, 2005

Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei. Fems Microbiology Letters 230(2): 275-282, 2004