title: Gene identification in a complex chromosomal continuum by local genomic cross-referencing.
abstract: Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of these repetitive DNAs are mobile and have homology to RNAs in various cell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservation and grass genome co-linearity as tools for gene identification. A bacterial artificial chromosome (BAC) clone containing sorghum genomic DNA was selected using a maize Adh1 probe. The 165 kb sorghum BAC was tested for hybridization to a set of clones representing the contiguous 280 kb of DNA flanking maize Adh1. None of the repetitive maize DNAs hybridized, but most of the low-copy-number sequences did. A low-copy-number sequence that did cross-hybridize was found to be a gene, while one that did not was found to be a low-copy-number retrotransposon that was named Reina. Regions of cross-hybridization were co-linear between the two genomes, but closer together in the smaller sorghum genome. These results indicate that local genomic cross-referencing by hybridization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Avramova
authors.forename: A
authors.initials: A
authors.lastname: Tikhonov
authors.forename: P
authors.initials: P
authors.lastname: SanMiguel
authors.forename: Y K
authors.initials: YK
authors.lastname: Jin
authors.forename: C
authors.initials: C
authors.lastname: Liu
authors.forename: S S
authors.initials: SS
authors.lastname: Woo
authors.forename: R A
authors.initials: RA
authors.lastname: Wing
authors.forename: J L
authors.initials: JL
authors.lastname: Bennetzen
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003001:Cloning, Molecular / Q000379:methods; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D003313:Zea mays / Q000235:genetics
chemical_list: D018744:DNA, Plant; D018626:Retroelements; D000426:Alcohol Dehydrogenase