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Scott J Emrich
Hui-Hsien Chou
Srinivas Aluru
Daniel A Ashlock
Patrick S Schnable
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doi:10.1534/genetics.106.064006
A more recent version of this article appeared on January 1, 2007.
REGULAR RESEARCH PAPERS |
Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution
Scott J Emrich 1, Li Li 1, Tsui-Jung Wen 1, Marna D Yandeau-Nelson 1, Yan Fu 1, Ling Guo 1, Hui-Hsien Chou 1, Srinivas Aluru 1, Daniel A Ashlock 2 and Patrick S Schnable 1*
1 Iowa State University
2 University of Guelph
* To whom correspondence should be addressed. E-mail: schnable{at}iastate.edu.
Submitted on August 3, 2006
Revised on September 14, 2006
Accepted on 19 October 2006
As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum of 10% over time. NIPs (Nearly Identical Paralogs) are defined as paralogous genes that exhibit >98% identity. Sequence analyses of the "gene space" of the maize inbred line B73 genome, coupled with wet lab validation, have revealed that conservatively at least ~1% of maize genes have a NIP, a rate substantially higher than in Arabidopsis. In most instances both members of maize NIP pairs are expressed and are therefore at least potentially functional. Of evolutionary significance members of many NIP families also exhibit differential expression. The finding that some families of maize NIPs are closely linked genetically while others are genetically unlinked is consistent with multiple modes of origin. NIPs provide a mechanism for the maize genome to circumvent the inherent limitation that diploid genomes can carry at most two "alleles" per "locus". As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species.
Key Words: Helitrons, MAGIs, Pack-MULEs, genome duplications, paralogs
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