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Evolutionary modes of emergence of short interspersed nuclear element ( SINE ) families in grasses
Author(s) -
Kögler Anja,
Schmidt Thomas,
Wenke Torsten
Publication year - 2017
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.13676
Subject(s) - biology , sine , genome , brachypodium , poaceae , brachypodium distachyon , genome evolution , genetics , oryza sativa , transposable element , hordeum vulgare , evolutionary biology , botany , gene , geometry , mathematics
Summary Short interspersed nuclear elements ( SINE s) are non‐autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINE s is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals ( Oryza sativa , Triticum aestivum , Hordeum vulgare , Panicum virgatum , Sorghum bicolor , Zea mays ) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species‐specific diversification and amplification. We found that Poaceae SINE s (PoaS) fall into two length categories: simple SINE s of up to 180 bp and dimeric SINE s larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty‐eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5′ or 3′ regions, across Poaceae species and share large sequence stretches with one or more other PoaS families.