Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes

Genome Biology
Dongying GaoScott Jackson

Abstract

Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood. Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa. We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that T...Continue Reading

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Citations

Mar 2, 2016·Genome Biology·Jonathan F WendelRod A Wing
Oct 27, 2017·Molecular Biology and Evolution·Dongying GaoScott A Jackson
Nov 22, 2017·The Plant Journal : for Cell and Molecular Biology·Ryan F McCormickJohn E Mullet
May 13, 2017·Nature Communications·Chuan XiaXiuying Kong
Jul 15, 2020·Proceedings of the National Academy of Sciences of the United States of America·Qinghua WangHugo K Dooner
Aug 9, 2019·International Journal of Molecular Sciences·Simon Orozco-AriasRomain Guyot
Apr 26, 2020·International Journal of Molecular Sciences·Ruslan KalendarAlan H Schulman
May 22, 2020·Plant Cell Reports·Diego ZavalloSebastian Asurmendi
Jan 27, 2021·Proceedings of the National Academy of Sciences of the United States of America·Shohei KojimaKeizo Tomonaga
Jun 25, 2021·Nucleic Acids Research·Frédéric Chaux-JukicZhou Xu

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Methods Mentioned

BETA
PCR

Software Mentioned

BLASTP
LTR
Repeat Masker
STRUC
FINDER
PAML
LTRdigest
LTRharvest
Bowtie2
dot plot

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