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Profiling of extensively diversified plant LINE s reveals distinct plant‐specific subclades
Author(s) -
Heitkam Tony,
Holtgräwe Daniela,
Dohm Juliane C.,
Minoche André E.,
Himmelbauer Heinz,
Weisshaar Bernd,
Schmidt Thomas
Publication year - 2014
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12565
Subject(s) - subclade , genome , retrotransposon , biology , computational biology , annotation , genetics , clade , evolutionary biology , phylogenetics , gene , transposable element
Summary A large fraction of eukaryotic genomes is made up of long interspersed nuclear elements ( LINE s). Due to their capability to create novel copies via error‐prone reverse transcription, they generate multiple families and reach high copy numbers. Although mammalian LINE s have been well described, plant LINE s have been only poorly investigated. Here, we present a systematic cross‐species survey of LINE s in higher plant genomes shedding light on plant LINE evolution as well as diversity, and facilitating their annotation in genome projects. Applying a Hidden Markov Model ( HMM )‐based analysis, 59 390 intact LINE reverse transcriptases ( RT s) were extracted from 23 plant genomes. These fall in only two out of 28 LINE clades (L1 and RTE ) known in eukaryotes. While plant RTE LINE s are highly homogenous and mostly constitute only a single family per genome, plant L1 LINE s are extremely diverse and form numerous families. Despite their heterogeneity, all members across the 23 species fall into only seven L1 subclades, some of them defined here. Exemplarily focusing on the L1 LINE s of a basal reference plant genome ( Beta vulgaris ), we show that the subclade classification level does not only reflect RT sequence similarity, but also mirrors structural aspects of complete LINE retrotransposons, like element size, position and type of encoded enzymatic domains. Our comprehensive catalogue of plant LINE RT s serves the classification of highly diverse plant LINE s, while the provided subclade‐specific HMM s facilitate their annotation.