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Transposable Elements in the Pineapple Genome

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.

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Correspondence to Ray Ming .

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Liu, J., Guyot, R., Ming, R. (2018). Transposable Elements in the Pineapple Genome. In: Ming, R. (eds) Genetics and Genomics of Pineapple. Plant Genetics and Genomics: Crops and Models, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-030-00614-3_11

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