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Composition and Organization of Major Repeat Components in the Brassica oleracea Genome

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The Brassica oleracea Genome

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

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Abstract

The release of the Brassica oleracea draft genome sequence opens numerous opportunities to understand its genome structure and evolution. A 515-Mb (82% of the total genome) high-quality draft assembly was made up of 56% repetitive elements (REs). Although the contribution of REs to genome structures, organization and evolution is relatively poorly understood, advances in bioinformatics have enabled genome-wide quantification and downstream analyses of REs in plant genomes. This chapter provides an overview of the classification, abundance, and genomic organization of the major types of REs that make up the main repeat component in the B. oleracea genome. Eight elements namely, 5S and 45S nrDNA, centromeric and subtelomeric tandem repeats (CentBo1, CentBo2, BoSTRa/b, and BoSTRc), a centromeric retrotransposon (BoCRB), and a Ty1/copia LTR retrotransposon (BoCopia-1) were classified into this repeat component. Whole-genome shotgun (WGS) mapping and molecular cytogenetic analyses provided an in-depth view of the abundance and distribution of these repeats both in the in silico generated draft assembly and mitotic metaphase chromosomes. The information not only validates the abundance of repeat elements in draft genomes, but also provide an avenue for understanding overall genome structure.

N. E. Waminal and S. Perumal—Equally contributed.

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Authors and Affiliations

  1. Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea

    Nomar Espinosa Waminal, Sampath Perumal, Jonghoon Lee & Tae-Jin Yang

  2. Bioscience Institute, Department of Chemistry and Life Science, Sahmyook University, Seoul, 01795, Republic of Korea

    Nomar Espinosa Waminal & Hyun Hee Kim

  3. Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada

    Sampath Perumal

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  1. Nomar Espinosa Waminal
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  3. Jonghoon Lee
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Correspondence to Tae-Jin Yang .

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  1. Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture of PRC, Wuhan, China

    Shengyi Liu

  2. Department of Plant Breeding Research Centre for BioSystems, Land Use, Justus Liebig University, Giessen, Germany

    Rod Snowdon

  3. Raja Ramanna Fellow, Government of India, ICAR-National Research Center on Plant Biotechnology, Pusa, New Delhi, India

    Chittaranjan Kole

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Waminal, N.E., Perumal, S., Lee, J., Kim, H.H., Yang, TJ. (2021). Composition and Organization of Major Repeat Components in the Brassica oleracea Genome. In: Liu, S., Snowdon, R., Kole, C. (eds) The Brassica oleracea Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-31005-9_5

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