Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 104, Issue 28, Pages 11844-11849Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0704258104
Keywords
gene distribution; gene number; genome annotation; repetitive DNA; sample sequencing
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Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains approximate to 37,000 candidate genes with homologues in other plant species. An additional approximate to 5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with approximate to 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.
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