ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2014
Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (International journal of molecular sciences · 2024Article
- The radish genome database (RadishGD): an integrated information resource for radish genomics.Database : the journal of biological databases and curation · 2019Article
- Transcriptional regulation of anthocyanin biosynthesis in a high-anthocyanin resynthesizedJournal of biological research (Thessalonike, Greece) · 2018Article
- Developmental Stage and Shape of Embryo Determine the Efficacy of Embryo Rescue in Introgressing Orange/Yellow Color and Anthocyanin Genes ofPlants (Basel, Switzerland) · 2018Article
- Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus).PloS one · 2018Article
- Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- Transcriptome sequencing and marker development for four underutilized legumes.Applications in plant sciences · 2015Article
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageThis manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.
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