title: Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.
abstract: 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 > or = 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 approximately 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.
authors.affiliation: Interdepartmental Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Emrich
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Tsui-Jung
authors.initials: TJ
authors.lastname: Wen
authors.forename: Marna D
authors.initials: MD
authors.lastname: Yandeau-Nelson
authors.forename: Yan
authors.initials: Y
authors.lastname: Fu
authors.forename: Ling
authors.initials: L
authors.lastname: Guo
authors.forename: Hui-Hsien
authors.initials: HH
authors.lastname: Chou
authors.forename: Srinivas
authors.initials: S
authors.lastname: Aluru
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Ashlock
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics*; D012641:Selection, Genetic; D012689:Sequence Homology, Nucleic Acid; D003313:Zea mays / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins