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Published online on July 5, 2007, 10.1073/pnas.0704258104
PNAS | July 10, 2007 | vol. 104 | no. 28 | 11844-11849


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BIOLOGICAL SCIENCES / PLANT BIOLOGY
A GeneTrek analysis of the maize genome

Renyi Liu*, Clémentine Vitte*, Jianxin Ma*, A. Assibi Mahama{dagger}, Thanda Dhliwayo{dagger}, Michael Lee{dagger}, and Jeffrey L. Bennetzen*,{ddagger}

*Department of Genetics, University of Georgia, Athens, GA 30602; and {dagger}Department of Agronomy, Iowa State University, Ames, IA 50011

Contributed by Jeffrey L. Bennetzen, May 7, 2007 (received for review March 19, 2007)

Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains {approx}37,000 candidate genes with homologues in other plant species. An additional {approx}5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with {approx}30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.

gene distribution | gene number | genome annotation | repetitive DNA | sample sequencing

Author contributions: R.L. and C.V. contributed equally to this work; R.L., C.V., J.M., and J.L.B. designed research; R.L., C.V., J.M., and A.A.M. performed research; R.L., C.V., J.M., A.A.M., T.D., M.L., and J.L.B. analyzed data; and R.L., C.V., M.L., and J.L.B. wrote the paper.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/cgi/content/full/0704258104/DC1.

{ddagger}To whom correspondence should be addressed. E-mail: maize{at}uga.edu

© 2007 by The National Academy of Sciences of the USA


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