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Logical Biology 9 (1):42-43, 2009 |
LETTER |
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http://im1.biz |
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© Truthfinding Cyberpress |
GENOME POLYLOIDY
CONFUSION |
How Many Genomes Does the Giant Bacterium Really Have?
Shi
V. Liu
4 Eagle Institute
of Molecular Medicine,
* Correspondence at SVL8EPA@gmail.com
(Received
HIGHLIGHT
A Letter
criticizing major flaws in a PNAS
publication claiming thousands of genomes in a bacterium but lacking
preservation of a single copy of completre data was rejected.
ABSTRACT
PNAS
published a discovery claiming of observing thousands of genomes in a
bacterium. This publication was
even covered by a news in Nature. However, demands for providing a
compelte set of data depicted in the publication have not been meet even after
over a year of repeated requests involving even two editors of PNAS. Now, when a scientific criticim on the
major flaws of this unverifiable publication was submitted to PNAS, the editorial board of PNAS rejected the criticism but gave no
reason, despite a clear request to PNAS
for showing specific reasons for rejection.
KEY WORDS
Giant bacterium, Thousands
genomes, Epulopiscium, Polyploidy,
Repeat, Flaws, Criticism, Protection
In their study published in PNAS, Mendell et al.(1) presented
evidence that “Epulopiscium contains tens of thousands of copies of its genome”
and stated that “polyploidy of the magnitude observed in Epulopiscium is
unprecedented”. This study actually
caught Nature’s attention which even
published a news with such a title as “Giant bacterium carries thousands of
genomes” (2).
However, upon careful evaluation of that publication I found
that the “thousands genomes” claim might be a severe misunderstanding and I
immediately requested the corresponding author to lend me their data for a
re-analysis (2). With the mediation of PNAS editors I received some data but the complete sets of data necessary
for my independent analysis of the published results summarized in various
tables and figures are still unavailable to me, despite repeated requests.
Thus, I have to base my criticisms on this high-profile PNAS publication on some logical and
conceptual reasoning.
What is shown in that study is actually a high-copy number
of some genes that were assumed to be “single-copy markers” (1). However, that “single-copy” assumption
might be invalid because even multiple copies of those single-copy genes were
detected in the “negative controls” – the surgeonfish gut contents without the
giant bacterium. Thus, if the same
logic used for generating “thousands of genomes for a giant bacterium” was
applied to estimate the genome number of the fish harboring these bacteria,
then a ridiculous conclusion of “small fish carries hundreds of genomes” may be
reached.
So
the whole study of this “genome polyploidy” was based on a wrong experimental
approach. Besides this
methodological mistake, there is also a deep conceptual misunderstanding on
genome number and chromosome polyploidy.
The genome of an organism is its hereditary information encoded in DNA
or RNA (3) and thus should always be just
one genome per organism. However, a
single complete genome may contain redundant information in various degrees
(short, medium, long repeats of DNA and organizations (dispersed repeats in a
single chromosome or distributed repeats in multiple chromosomes). But that DNA fragment repetition or
chromosome polyploidy should not be confused with genome redundancy or even
extreme genome polyploidy.
Because
this PNAS publication reached a wrong
conclusion from a largely inappropriate research approach, it should be retracted
to avoid further confusion in the scientific literature.
Shi V. Liu
Eagle Institute of Molecular
Medicine
Apex, NC
27502 USA
References
1. Mendell
JE, Clements KD, Choat JH, & Angert ER (2008) Extreme polyploidy in a large
bacterium. Proc Natl Acad Sci U S A 105, 6730-6734.
2. Ledford
H (2008) Giant bacterium carries thousands of genomes. Nature News http://www.nature.com/news/2008/080508/full/news.2008.806.html.
3. Anonymous
(2009) Genome. Wikipedia.
* This Letter was submitted to PNAS
on June 2, 2009 but was rejected by PNAS
on June 11, 2009 (see appendixes below).
The publication here is the same as submitted to PNAS except for the added highlight, abstract and key wrods.
Appendixes
1.
Cover letter to PNAS
June 2nd, 2009
Dear
PNAS Editors,
I am submitting a Letter entitled “How many genomes
does the giant bacterium really have?” It contains only 377 words in the body
and 3 references.
I wish to point
out that, although this Letter addresses a publication that is over a year old,
it is still a legitimate submission because the delay for its writing is caused
by the delay in providing necessary data for independent analysis. If the author had provided the data
reported in their publication in the timely fashion, then this Letter should be
submitted long time ago.
Unfortunately,
even with successively mediation by two editors from PNAS, the corresponding author still has not provided me with the
complete data set. It is really
ironic that a very important study demonstrating an “unprecedented”
polyploidy – “tens of thousands of copies of genome” in a bacterium just have
ONE copy of the data in only the hands of a junior student author and that data
is even difficult to get even thought it should be ready for inspection at any
time after its publication.
More detailed
information on communications with the authors and the PNAS editors can be provided, if they are indeed necessary.
Sincerely yours,
Shi V. Liu
MD PhD
Eagle Institute of Molecular Medicine
Apex, NC 27502, USA
2.
Rejection from PNAS
June 11, 2009
Title: "How many genomes does the giant bacterium really have?"
Tracking #:
2009-06093
Authors: Liu
Dear Dr. Liu,
I regret to inform you that the PNAS Editorial Board has declined to publish
your Letter to the Editor.
Thank you for submitting your comments to PNAS.
Sincerely yours,
Randy
Schekman
Editor-in-Chief
3.
A request
for reasons for the rejection
Dear PNAS
Editor-in-Chief,
I need to
know WHY?