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Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains [approximately equal to] 37,000 candidate genes with homologues in other plant species. An additional [approximately equal to] 5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with [approximately equal 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. gene distribution | gene number | genome annotation | repetitive DNA | sample sequencing

Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains ≈37,000 candidate genes with homologues in other plant species. An additional ≈5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with ≈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. [ABSTRACT FROM AUTHOR]