How many genomes are enough? The more, the merrier, researchers declare. Is the sky the limit? By
Tabitha M Powledge
How many sequenced genomes are enough? The minimum number for comparative genomics, researchers say,
depends on what you want to learn. The optimum number is a still a mystery.
For identifying cis-regulatory regions such as enhancers and promoters, the genomes of three species
that are roughly equidistant evolutionarily is the bare minimum, and more is better, according to
Lincoln Stein. Stein, who is at Cold Spring Harbor Laboratory, is first author of a paper on the
Caenorhabditis briggsae genome in the first issue of PLoS Biology, an open-access online journal
published by the Public Library of Science. He pointed out that having the genomes of at least three
species permits distinguishing between the signal-bases conserved because they actually do something-
and noise-bases conserved simply because they haven't mutated yet. "As you add more species to the
alignment, the signal remains the same while the noise decreases because there are fewer and fewer
bases that are the same because of an accident of history," he told The Scientist.
Read the rest from The Scientist.com biomedcentral.com07Open ↗
Caenorhabditis comparative genomics The C. briggsae draft genome strengthens the case for sequencing
additional worm species By Cathy Holding
Comparative genomic analysis of closely related organisms yields considerably more information on
the structure and regulation of genes than that garnered by gene prediction programs. In the October
Public Library of Science Biology, Lincoln Stein at Cold Spring Harbor (CSH) and 35 collaborators
from 13 other research centers report the sequencing of the Caenorhabditis briggsae genome. The
data, when used in comparison with the
C. elegans genome, yield not only a great deal of structural and functional detail, but also
unexpected information on the mechanisms and effects of genome evolution (Public Library of
Science Biology, October 2003).
Jane Rogers, head of sequencing at the Sanger Institute-one of the collaborating centers-explained
the choice of sequencing method for the genome. Whole genome shotgun reads combined with a high-
resolution physical map were integrated with the previously finished clone-based sequence. "We had
only had experience of using a whole genome shotgun approach for relatively small genomes (5-10 Mb).
However, Celera had reported a successful assembly of the Drosophila genome, and with the reference
sequence of C. elegans available, we felt confident that a whole genome assembly would be feasible.
The project provided a test-bed for Phusion, a new assembler, developed at the Sanger Institute by
Jim Mullikin." This technique produced a draft sequence of the C. briggsae genome containing 102 Mb
of DNA sequence, representing about 98% of the genome.
Shortening LINEs Internal polyadenylation signals in mobile genetic elements limits their mobility
By Cathy Holding
LINE-1 (L1) elements are the mammalian version of autonomously replicating retrotransposable
elements active via an RNA intermediate that lack long terminal repeats. They are very ancient,
dating back about 100 million years, and distinctive families containing many thousands of members
are found in plants, fungi, invertebrates, and vertebrates. Because of their ability to amplify
themselves, they constitute about 30% of genomic DNA in mammals, and their mobility within the
genome coupled with their disruptive effects have affected the evolution, structure, and function of
mammalian genomes. L1 expression is elevated in certain cancers, reflecting a lack of control over
both expression regulation and genetic damage.
In the November 16 Nature Genetics, Victoria Perepelitsa-Belancio and Prescott Deininger at the
Tulane University Health Sciences Center report the discovery of the use of multiple canonical and
noncanonical polyadenylation (polyA) sites in the A-rich region of L1 sequences in a cell- and tissue-
specific fashion that limit the spread and consequent genetic damage of retrotransposons, revealing
both a transposon survival mechanism and a previously unrecognized method of mRNA regulation by
means of conventional 3' end formation in mammalian cells (Nature Genetics, DOI:10.1038/ng1269,
November 16, 2003).
Kind Regards, Robert Karl Stonjek.