Page 5 - Genomics and Applied Biology

Genomics and Applied Biology, 2010, Vol.1 No.3
http://gab.sophiapublisher.com
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“salicoid duplication”, and the 19 haploid
chromosomes in poplar genome might evolve from
10 ancestral chromosomes (Tuskan et al., 2006).
Meanwhile, the comparative mapping project
demonstrated that the genomes of different poplar
species maintained the basic genome structure formed
by the salicoid duplication event (Yin et al., 2008).
Compare to these findings, gene distribution is also an
important aspect to explore the characteristics of
poplar genome. Relating to this point, there was only
a short descriptive paragraph in the poplar genome
paper, but no statistical analyses were conducted in
that article (Tuskan et al., 2006). In this paper, the
Poisson calculator is employed to survey gene density
on different chromosomes of poplar genome. In this
study, we especially address on two interesting
questions: first, do the duplicated chromosomes have
the similar gene density? Second, how many percent
of genes in poplar genome can be captured by a
moderate scale EST sequencing project?
1 Results
1.1 Compare gene densities between chromo-
somes that share large duplicated segments
Based on the Poisson calculator, genes were found to
occur at different frequency on different chromosome
members. Six chromosomes, including chromosome
Ⅱ , Ⅵ , Ⅷ , Ⅸ , Ⅹ , and XV, were found to be
overabundant with genes; eight of them, including
chromosome Ⅰ, Ⅳ, Ⅺ , Ⅻ, XIII, XVII, XVIII, and
XIX, were sparse with genes; only four chromosomes,
including chromosome Ⅲ, Ⅴ , XIV, and XVI, had
gene quantities that didn’t significantly apart from the
expected numbers (table 1). Therefore, chromosomes
can be classified into three classes based on the gene
density: chromosomes with more genes than the
expected numbers; chromosomes with genes quantity
that do not significantly apart from the expected
numbers; chromosomes with less genes than the
expected numbers.
Visual plotting of gene distribution within each
chromosome and homology among chromosome
members of poplar genome were displayed in figure
1. From this figure, we found that genes distributed
relatively evenly within each chromosome. We
didn’t detect regions with low gene density that
might correspond to the centromeric and telomeric
regions. Since the current sequence scaffolds
mapped onto different chromosomes only account
86% of the total poplar genome and repetitive
sequences tend to be more difficult to be assembled
in the shotgun sequencing project, we proposed
these regions might embed in the sequence scaffolds
that hadn’t mapped onto chromosomes.
Referring to the poplar genome paper (Tuskan et al.,
2006), the 19 haploid chromosomes of poplar
genome were duplicated from 10 ancestral
chromosomes. However, the pattern of
chromosomes overabundant, even, or sparse with
genes is different from the chromosomal
homologous pattern as revealed by Tuskan and his
colleagues (Tuskan et al., 2006). We compare eight
pairs of chromosomes that share large duplication
segments (table 2) and find that only gene densities
on two pairs of the chromosomes are in the same
class, whereas gene densities on the other six
homologous pairs of chromosomes are in different
classes. For example, chromosome Ⅻ and XV are
in high homology, but their gene densities are in
opposite classes. Chromosome XII is overabundant
with genes. By contrast, chromosome XV is sparse
with genes.
1.2 Survey gene models captured by ESTs
Genome can be classified into intergenic and genic
regions. Genic region is consisted of 5’UTR, exons,
introns, and 3’ UTR and the regulatory elements.
When a gene is transcribed into mature mRNA, its
introns were splice off. Gene sequences that can be
captured by EST sequencing would include the 5’
UTR, exons, and 3’ UTR. In this study, we total
investigate 29 934 putative genes. The average