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Genomic Survey of the Hidden Components of the B. rapa Genome

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The Brassica rapa Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

The sequencing of the Brassica rapa genome has enabled better understanding of its structure and evolution, and created numerous opportunities for exploration of genome function and breeding applications. Nevertheless, the currently available completed genome sequences are estimated to cover only about 60 % of the genome, while the remaining 40 % is unassembled mainly due to the highly repetitive nature of this portion of the genome. Elucidation of the nature and distribution of repeat elements in the context of the entire genome would enhance our understanding of their role in genome structure, function, and evolution. In this chapter, we review the genomic distribution, characterization and evolutionary implications of currently identified repeat elements comprising the ‘hidden’ portion of the B. rapa genome. Low-coverage whole-genome sequence (WGS) was used to survey the major genomic repeats and their proportion in the B. rapa genome. Coupling this with molecular cytogenetics, we characterized the abundance and genomic distribution of seven major repeats, namely centromeric tandem repeats 1 and 2, centromeric retrotransposons, pericentromeric retrotransposons, 5S rDNA, 45S rDNA, and subtelomeric tandem repeats. These repeats accounted for approximately 20 % of the B. rapa genome, which is much more than the <1 % covered by repeats in the currently available genome assembly. We also compared their distributions among different B. rapa accessions and in the close relative Brassica oleracea, for better understanding of the plasticity of the Brassica genomes.

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Acknowledgments

This research was carried out with the support by Golden Seed Project (Center for Horticultural Seed Development, No. 213003-04-3-SB430), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS), Republic of Korea.

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Authors and Affiliations

  1. Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Nomar Espinosa Waminal, Sampath Perumal & Tae-Jin Yang

  2. Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Korea

    Ki-Byung Lim

  3. National Academy of Agricultural Science, Rural Development Administration, 150 Suinro, Suwon, 441-707, Republic of Korea

    Beom-Seok Park

  4. Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 139-742, Republic of Korea

    Hyun Hee Kim

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  1. Nomar Espinosa Waminal
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  2. Sampath Perumal
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  3. Ki-Byung Lim
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  4. Beom-Seok Park
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  5. Hyun Hee Kim
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  6. Tae-Jin Yang
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Correspondence to Tae-Jin Yang .

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Editors and Affiliations

  1. Chinese Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Beijing, China

    Xiaowu Wang

  2. Department of Genetics & Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, India

    Chittaranjan Kole

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Waminal, N.E., Perumal, S., Lim, KB., Park, BS., Kim, H.H., Yang, TJ. (2015). Genomic Survey of the Hidden Components of the B. rapa Genome. In: Wang, X., Kole, C. (eds) The Brassica rapa Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-47901-8_7

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