title: The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm.
abstract: TRIMs (terminal-repeat retrotransposons in miniature), which are characterized by their small size, have been discovered in all investigated vascular plants and even in animals. Here, we identified a highly conservative TRIM family referred to as Wukong elements in the maize genome. The Wukong family shows a distinct pattern of tandem arrangement in the maize genome suggesting a high rate of unequal crossing over. Estimation of insertion times implies a burst of retrotransposition activity of the Wukong family after the allotetraploidization of maize. Using next-generation sequencing data, we detected 87 new Wukong insertions in parents of the maize NAM population relative to the B73 reference genome and found abundant insertion polymorphism of Wukong elements in 75 re-sequenced maize lines, including teosinte, landraces, and improved lines. These results suggest that Wukong elements possessed a persistent retrotransposition activity throughout maize evolution. Moreover, the phylogenetic relationships among 76 maize inbreds and their relatives based on insertion polymorphisms of Wukong elements should provide us with reliable molecular markers for biodiversity and genetics studies.
authors.affiliation: Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China.
authors.forename: Tingzhang
authors.initials: T
authors.lastname: Wang
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854.
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
authors.affiliation: Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China jhxu@zju.edu.cn.
authors.forename: Jian-Hong
authors.initials: JH
authors.lastname: Xu
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D018744:DNA, Plant / Q000737:chemistry / Q000378:metabolism; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics*; D003313:Zea mays / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D018626:Retroelements
keywords: NGS; TRIM; insertion polymorphism; maize (Zea mays); retrotransposon