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Comprehensive analyses of micro RNA gene evolution in paleopolyploid soybean genome
Author(s) -
Zhou Zhengkui,
Wang Zheng,
Li Weiyu,
Fang Chao,
Shen Yanting,
Li Congcong,
Wu Yunshuai,
Tian Zhixi
Publication year - 2013
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.12293
Subject(s) - gene , genome , biology , genetics , rna , computational biology
Summary mi RNA genes are thought to undergo quick birth and death processes in genomes and the emergence of a MIRNA ‐like hairpin provides the base for functional mi RNA gene formation. However, the factors affecting the formation of an active mi RNA gene from a MIRNA ‐like hairpin within a genome remain unclear. We performed a genome‐wide investigation of MIRNA ‐like hairpin accumulation, expression, structural changes and relationships with annotated genomic features in the paleopolyploid soybean genome. Our results showed that adjacent gene and transposable element content, rates of genetic recombination at location of emergence, along with its own gene structure divergence greatly affected mi RNA gene evolution. Further investigation suggested that mi RNA genes from different duplication sources followed distinct evolutionary trajectories and that the accumulation of MIRNA ‐like hairpins might be an important factor in causing long terminal repeat retrotransposons to lose activity during genome evolution.