title: B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.).
abstract: BACKGROUND
  The dispensable maize (Zea mays L.) B chromosome is highly heterochromatic and widely believed to be devoid of functional genes. Although low-copy B chromosome causes no obvious phenotype variation, its existence might influence A genome gene expression. Previous studies suggested that B chromosomes are evolved from standard chromosomes; therefore, they might contain genic regions showing homology with A chromosome sequences.
  
  
  RESULTS
  Our data suggested that maize B chromosome influences the A-genome transcription with stronger effect associated with an increase in copy number of B chromosome. In total 130 differently expressed genes were detected in comparison between with and without B chromosome lines. These differentially expressed genes are mainly involved in cell metabolism and nucleotide binding. Using Starter + B, we amplified ten B chromosome loci with high sequence similarity to A-genome genes. Fluorescence in situ hybridization (FISH) confirmed that at least four ~5 kb-sized genes are located on the B chromosome. In addition, through de novo assembly of the reads not unmapped to maize B73 reference genome together with PCR validation, we found three B-located LTR; in particular, one of them, the 3.2 kb comp75688, is expressed in a B-dosage dependent manner.
  
  
  CONCLUSIONS
  We found that in the presence of maize B chromosome, the transcription of A genome genes was altered, with more impact by the increase of the B chromosome number. The B-located transcriptionally active genes showed high similarity to their A-genome homologues, and retrotransposons on B chromosome also have partial homologous to A genome sequences. Our data shed more lights on the genome structure and evolution of the maize B chromosome.
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Du
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. weiweijin@cau.edu.cn.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Jin
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D006570:Heterochromatin / Q000235:genetics; D054643:INDEL Mutation; D017404:In Situ Hybridization, Fluorescence; D020641:Polymorphism, Single Nucleotide; D011544:Pseudogenes / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*
chemical_list: D006570:Heterochromatin
keywords: B chromosome; Evolution; Maize; RNA-seq; Transcription