A GeneTrek analysis of the maize genome

Proceedings of the National Academy of Sciences of the United States of America - Tập 104 Số 28 - Trang 11844-11849 - 2007
Renyi Liu1, Clémentine Vitte1, Jianxin Ma1, A. Assibi Mahama2, Thanda Dhliwayo2, Michael Lee2, Jeffrey L. Bennetzen1
1*Department of Genetics, University of Georgia, Athens, GA 30602; and
2ISU - Iowa State University (Ames, Iowa 50011 - United States)

Tóm tắt

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.

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Proceedings of the National Academy of Sciences of the United States of America

Tập 104 Số 28

11844-11849

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