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Papaya Repeat Database

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Genetics and Genomics of Papaya

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 10))

Abstract

In this chapter, we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly arrayed sequences, and high copy number genes. These repetitive sequences account for ~56 % of the papaya genome, with TEs being the most abundant at 52 %, tandem repeats at 1.3 %, and high copy number genes at 3 %. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40 % of the genome. The most prevalent retrotransposons are Ty3–gypsy (27.8 %) and Ty1–copia (5.5 %). Among the tandem repeats, microsatellites are the most abundant in number but represent only 0.19 % of the genome. Minisatellites and satellites are less abundant but represent 0.68 and 0.43 % of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (>2 %) are present in large gene families with copy number greater than 20. Papaya sex chromosomes are significantly enriched of a repertoire of repetitive sequences, and the male-specific region expanded by massively accumulation of repeated DNA, representing 83 % (mostly TE), while the corresponding X region included 70 % of such repeats. In an effort to integrate all the information, we provide here the pipeline to gather and process data related to repetitive elements in papaya.

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Authors and Affiliations

  1. Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore

    Niranjan Nagarajan

  2. Facultad de Ciencias, Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, Granada, 18071, Spain

    Rafael Navajas-Pérez

Authors
  1. Niranjan Nagarajan
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  2. Rafael Navajas-Pérez
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Correspondence to Rafael Navajas-Pérez .

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Editors and Affiliations

  1. Department of Plant Biology, University of Illinois at Urbana-Champai, Urbana, Illinois, USA

    Ray Ming

  2. Hawaii Agriculture Research Center, Kaneohe, Hawaii, USA

    Paul H. Moore

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Nagarajan, N., Navajas-Pérez, R. (2014). Papaya Repeat Database. In: Ming, R., Moore, P. (eds) Genetics and Genomics of Papaya. Plant Genetics and Genomics: Crops and Models, vol 10. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8087-7_13

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