title: Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping.
abstract: BACKGROUND
  Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9-11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear.
  
  
  RESULTS
  About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea.
  
  
  CONCLUSIONS
  The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work.
authors.forename: Zexi
authors.initials: Z
authors.lastname: Cai
authors.forename: Huijun
authors.initials: H
authors.lastname: Liu
authors.forename: Qunyan
authors.initials: Q
authors.lastname: He
authors.forename: Mingwei
authors.initials: M
authors.lastname: Pu
authors.forename: Jian
authors.initials: J
authors.lastname: Chen
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Lai
authors.forename: Xuexian
authors.initials: X
authors.lastname: Li
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing 100193, China. weiweijin@cau.edu.cn.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Jin
mesh_terms: D002503:Centromere; D032461:Chromosomes, Plant; D031742:Coix / Q000145:classification / Q000235:genetics*; D004276:DNA, Satellite; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics; D006824:Hybridization, Genetic; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D005810:Multigene Family; D010802:Phylogeny; D011003:Ploidies; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D020079:Terminal Repeat Sequences
chemical_list: D004276:DNA, Satellite; D018626:Retroelements