Gene identification in a complex chromosomal continuum by local genomic cross-referencing

Zoya Avramova, Alexander Tikhonov, Phillip SanMiguel, Young Kwan Jin, Changnong Liu, Sung Sick Woo, Rod A. Wing, Jeffrey L. Bennetzen

Research output: Contribution to journalArticle

50 Citations (Scopus)

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 gens 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.

Original languageEnglish (US)
Pages (from-to)1163-1168
Number of pages6
JournalPlant Journal
Volume10
Issue number6
DOIs
StatePublished - Dec 1996

Fingerprint

Sorghum
Genome
genomics
genome
Sorghum (Poaceae)
DNA
Zea mays
Bacterial Artificial Chromosomes
bacterial artificial chromosomes
hybridization
Clone Cells
Genes
clones
genes
corn
Retroelements
retrotransposons
Poaceae
RNA
grasses

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Avramova, Z., Tikhonov, A., SanMiguel, P., Jin, Y. K., Liu, C., Woo, S. S., ... Bennetzen, J. L. (1996). Gene identification in a complex chromosomal continuum by local genomic cross-referencing. Plant Journal, 10(6), 1163-1168. https://doi.org/10.1046/j.1365-313X.1996.10061163.x

Gene identification in a complex chromosomal continuum by local genomic cross-referencing. / Avramova, Zoya; Tikhonov, Alexander; SanMiguel, Phillip; Jin, Young Kwan; Liu, Changnong; Woo, Sung Sick; Wing, Rod A.; Bennetzen, Jeffrey L.

In: Plant Journal, Vol. 10, No. 6, 12.1996, p. 1163-1168.

Research output: Contribution to journalArticle

Avramova, Z, Tikhonov, A, SanMiguel, P, Jin, YK, Liu, C, Woo, SS, Wing, RA & Bennetzen, JL 1996, 'Gene identification in a complex chromosomal continuum by local genomic cross-referencing', Plant Journal, vol. 10, no. 6, pp. 1163-1168. https://doi.org/10.1046/j.1365-313X.1996.10061163.x
Avramova, Zoya ; Tikhonov, Alexander ; SanMiguel, Phillip ; Jin, Young Kwan ; Liu, Changnong ; Woo, Sung Sick ; Wing, Rod A. ; Bennetzen, Jeffrey L. / Gene identification in a complex chromosomal continuum by local genomic cross-referencing. In: Plant Journal. 1996 ; Vol. 10, No. 6. pp. 1163-1168.
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