Originally published as Genetics Published Articles Ahead of Print on November 16, 2006.

Genetics, Vol. 175, 429-439, January 2007, Copyright © 2007
doi:10.1534/genetics.106.064006

Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution

Scott J. Emrich^*,,1, Li Li^,,1, Tsui-Jung Wen^**,2, Marna D. Yandeau-Nelson^,,3, Yan Fu^,,4, Ling Guo^*,, Hui-Hsien Chou^*,,,,***, Srinivas Aluru^*,,,,***, Daniel A. Ashlock^*,***,,5 and Patrick S. Schnable^{*,,,**,,,***,6}

^* Interdepartmental Bioinformatics and Computational Biology Graduate Program, Department of Electrical and Computer Engineering, Interdepartmental Plant Physiology Graduate Program, Department of Genetics, Development and Cell Biology, ^** Department of Agronomy, Interdepartmental Genetics Graduate Program, Department of Computer Science, Center for Plant Genomics, ^*** L. H. Baker Center for Bioinformatics and Biological Statistics and Department of Mathematics, Iowa State University, Ames, Iowa 50011

⁶ Corresponding author: 2035B Roy J. Carver Co-Laboratory, Iowa State University, Ames, IA 50011-3650.
E-mail: schnable{at}iastate.edu

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. Nearly identical paralogs (NIPs) 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 that 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.

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