Differentiation of Gene Richness on Duplicated Chromosomes and Survey of Genes Captured by ESTs in Poplar Genome  

Shuxian Li , Xiaogang Dai , Handong Gao , Tongming Yin
Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing, 210037;
The Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, 210037
Author    Correspondence author
Genomics and Applied Biology, 2010, Vol. 1, No. 3   doi: 10.5376/gab.2010.01.0003
Received: 16 Oct., 2010    Accepted: 09 Nov., 2010    Published: 29 Dec., 2010
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Preferred citation for this article:

Li et al., 2010, Differentiation of Gene Richness on Duplicated Chromosomes and Survey of Genes Captured by ESTs in Poplar Genome, Genomics and Applied Biology, 29(3): 570-576 (DOI: 10.3969/gab.029.000570)

Abstract

In higher plant genomes, most sequences are unexpression sequence, the proportion of a genome that encodes for genes may be very small. Understanding gene distribution in the genome is a very important aspect for invastigating the genome structure. Funded by the U.S. Department of Energy, a clonal Populus trichocarpa genome sequencing has been completed and released to the public. The accomplishment of poplar genome offers us a unique opportunity to survey the gene distribution in the genome of a forest tree. In this paper, based on Poisson calculator, we investigated the gene density of various chromosomes in poplar genome. As a result, we found that gene density is significantly different among chromosomes in poplar genome. Modern poplar genome arose from an ancient whole genome duplication event, known as “salicoid duplication”. Thus poplar genome shared large duplication segments among different chromosome members. However, our results demonstrated that gene abundance pattern was different from the chromosomal duplication pattern of poplar genome. This implied the duplicated genes lost at different rates on the duplicated chromosomes following the salicoid duplication. Meanwhile, based on alignment with about 90 thousands ESTs,we found that only 16.8% of the predicted gene models in poplar genome had EST proofs. Although, EST sequencing is an attractive alternative to whole genome sequencing for gene identification, the power of small scale EST sequencing study should be properly evaluated since with limited number of EST sequences, genes captured by ESTs are fairly limited.

Keywords
Poplar genome; Gene distribution; EST coverage; Salicoid duplication event
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