title: Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads.
abstract: Haplotype variation not only involves SNPs but also insertions and deletions, in particular gene copy number variations. However, comparisons of individual genomes have been difficult because traditional sequencing methods give too short reads to unambiguously reconstruct chromosomal regions containing repetitive DNA sequences. An example of such a case is the protein gene family in maize that acts as a sink for reduced nitrogen in the seed. Previously, 41-48 gene copies of the alpha zein gene family that spread over six loci spanning between 30- and 500-kb chromosomal regions have been described in two Iowa Stiff Stalk (SS) inbreds. Analyses of those regions were possible because of overlapping BAC clones, generated by an expensive and labor-intensive approach. Here we used single-molecule real-time (Pacific Biosciences) shotgun sequencing to assemble the six chromosomal regions from the Non-Stiff Stalk maize inbred W22 from a single DNA sequence dataset. To validate the reconstructed regions, we developed an optical map (BioNano genome map; BioNano Genomics) of W22 and found agreement between the two datasets. Using the sequences of full-length cDNAs from W22, we found that the error rate of PacBio sequencing seemed to be less than 0.1% after autocorrection and assembly. Expressed genes, some with premature stop codons, are interspersed with nonexpressed genes, giving rise to genotype-specific expression differences. Alignment of these regions with those from the previous analyzed regions of SS lines exhibits in part dramatic differences between these two heterotic groups.
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854;
authors.forename: Jiaqiang
authors.initials: J
authors.lastname: Dong
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854;
authors.forename: Yaping
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854;
authors.forename: Dibyendu
authors.initials: D
authors.lastname: Kumar
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854;
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zhu
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.affiliation: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854; messing@waksman.rutgers.edu.
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D018628:Gene Dosage; D017343:Genes, Plant; D018745:Genome, Plant; D006239:Haplotypes; D017422:Sequence Analysis, DNA / Q000379:methods; D003313:Zea mays / Q000235:genetics*
chemical_list: D018744:DNA, Plant
keywords: gene copy number; haplotype variation; maize genome; shotgun DNA sequencing; transposable elements