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Genomics and Applied Biology, 2010, Vol.1 No.3
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An Analysis Open Access
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
Corresponding author, tmyin@njfu.com.cn;
Authors
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
This article was first published in Genomics and Applied Biology (Regular Print Version), and here was authorized to redistribute under the terms of the Creative Commons
Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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 investigating 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
Background
Forests are the principal representatives of the
terrestrial ecosystem and provide important
sustainable resources for humankind (Li and Yin,
2007). Although forests only cover about 30% of the
earth’s land surface, they allocated over 80% of CO2
from the atmosphere through green vegetations. Thus,
increasing forest productivity is also an essential
approach to reduce the greenhouse gas. However, our
understanding for forest trees is limited in comparison
with that for many other organisms, and better
understanding of the genetic mechanisms influencing
tree adaptation and productivity is important for the
management of the world’s forest resources
(Caetano-Anollés and Gresshoff, 1997). The genus
Populus
possesses many characteristics that are
conductive to functional genomics, which leads the
emergency of poplar as the model system for tree
genome research (Wullschleger et al., 2002). Under
the efforts of numerous scientists worldwide, the
genome of a black cottonwood (
Populus trichocarpa
Torr. & Gray ex Brayshaw), “clone 383-2499”, has
been sequenced and publicly released (Tuskan et al.,
2006). It is the first sequence of a woody perennial
plant.
In recent decades, sequencing capacity available to
biological scientist increases in an exponential
manner. Several plant genomes have been sequenced
(Lyons and Freeling, 2008). However, whole genome
sequences for most plant species are still unavailable
in the near future, especially for tree species. The
genome sequence of poplar offers us a unique
opportunity to learn the genome characteristics of a
tree species. In the earlier studies, scientists have
discovered many interesting findings, for example,
the poplar genome project revealed that the
chromosomes of modern
Populus
arose from an
ancient whole-genome duplication event known as