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Transposable Elements in the Pineapple Genome

  • Juan Liu
  • Romain Guyot
  • Ray MingEmail author
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)

Abstract

Transportable elements (TEs) account for majority of genomic sequences in most plant genomes. They play vital roles in the structure, function, and evolution of genomes. Pineapple (Ananas comosus L.) is an important fruit crop performing CAM photosynthesis and has a relatively small genome size at 526 Mb. But it contains relative high proportion of TEs. In pineapple genome, TEs constitute 44% of the genome assembly and 69% of the genome after adding 25% of unassembled TEs. LTR (long terminal repeat) retrotransposons in Class I (retrotransposons) are the most abundant TEs in pineapple, accounting for 32% of the genome assembly. Class I TEs tend to enriched in gene-poor regions, while Class II TEs tend to enriched in gene-rich regions. The distribution of LTR retrotransposons among pseudo-molecules varies, ranging from 22.16 to 33.18%. A negative correlation is detected between LTRs copy number and expression levels. In addition, TEs of different families show expression bias in various tissues. The Sira family was most highly expressed in flower and floral tissues. The massive expansion of several TE families affects the genome size rapidly. Del, a family of the Gypsy superfamily, constitute of 60% of LTR retrotransposons. The insertion time suggests that it amplified to very high copy number at about 1.5–2.0 million years ago. In this chapter, we will review the resent discovered TEs in the pineapple genome.

Keywords

Transportable elements LTR retrotransposons Pineapple Genome evolution Expression level 

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Institut de recherche pour le développement (IRD)CIRAD, Université de MontpellierMontpellierFrance
  3. 3.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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