Unleashing the Genome of Brassica Rapa

Overview

Journal Front Plant Sci

Date 2012 Aug 7

PMID 22866056

Citations 24

Authors

Haibao Tang

Eric Lyons

Affiliations

Soon will be listed here.

Abstract

The completion and release of the Brassica rapa genome is of great benefit to researchers of the Brassicas, Arabidopsis, and genome evolution. While its lineage is closely related to the model organism Arabidopsis thaliana, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, Brassica's genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the Brassica paleohexaploidy is characterized, syntenic regions with A. thaliana are identified, and the TOC1 gene in the circadian rhythm pathway from A. thaliana is used to find duplicated orthologs in B. rapa. These TOC1 genes are further analyzed to identify conserved non-coding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each "cookbook style" analysis includes a step-by-step walk-through with links to CoGe to quickly reproduce each step of the analytical process.

Citing Articles

DNA methylation dynamics in male germline development in Brassica Rapa.

Zhang J, Wu D, Zhang Y, Feng X, Gao H Mol Hortic. 2025; 5(1):16.

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Developing genomic tools to assist turnip rape [ (L.) subsp. (DC.) Metzg.] breeding.

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Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs).

Amas J, Bayer P, Hong Tan W, Tirnaz S, Thomas W, Edwards D Plant Biotechnol J. 2023; 21(10):2100-2112.

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Genomic Blocks in Support Arabideae as Next Diverging Clade in Brassicaceae.

Walden N, Nguyen T, Mandakova T, Lysak M, Schranz M Front Plant Sci. 2020; 11:719.

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Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa.

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