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ECCB 2014 Accepted Poster with Abstract F: Evolution and population genomics; F03: Alienness: Rapid detection of horizontal gene transfers in metazoan genomes

Authors:

Abstract

Horizontal gene transfer (HGT) is the transmission of genetic material between species by ways other than direct (vertical) inheritance from parents to the offspring. HGT is recognized as a major evolutionary force in prokaryotes as it is involved in acquisition of antibiotic resistance or pathogeny. HGT has long been overlooked and considered insignificant in eukaryotes. However, HGT have also played important roles in the evolutionary history and biology of these species, including animals. For example, HGT have contributed to the colonization of land by plants, in the emergence of plant parasitism in nematodes or in the development of capabilities like resistance to extreme temperatures or desiccation. Progress in genome sequencing technologies has allowed multiple animal genomes to be publicly released. Systematic searches for HGT events in the root-knot nematodes or in the bdeloid rotifer, have shown that between 3 and 9 % of protein-coding genes in these species were of foreign origin (1). However, in the absence of a user-friendly, rapid and publicly available tool to detect HGT events in metazoan genomes, we still lack a global view of the prevalence of HGT in animals. Here, we propose a tool that allows automatic detection of putative HGT events, based on the predicted protein set from a genome or transcriptome. Our tool has been specifically designed to rapidly detect genes of non-metazoan origin (e.g. bacterial, fungal) in metazoan genomes (e.g. insects, mammals, nematodes). Based on a blastP search against the NCBI's non-redundant library (nr), we retrieve putative homologs for each protein query in a whole proteome. Canonical metazoan proteins should return better blast hits to metazoans than to non-metazoans. Conversely, candidate HGT of non-metazoan origin are expected to return better blast hits to non-metazoans than metazoans. Our method uses the Alien Index metrics as described in (2) to detect a significant gap between the best metazoan and non-metazoan e-values as an indicator of putative HGT. An Alien Index (AI) > 0, indicates a better hit to non-metazoans than to metazoans. An AI > 30 corresponds to a difference of magnitude > e10 between the best non-metazoan and metazoan e-values and is estimated to be a clear indication of HGT. The main difficulty of this approach is to automatically retrieve taxonomic information and to assign a hit to either metazoan, or non-metazoan categories. Our methods not only allows classifying best blast hits in metazoans and non-metazoans but it further classifies non-metazoan best hits into virus, bacteria, archaea, fungi, plant and "other". Thus it allows both the detection of putative HGT acquisitions and identification of the putative donors.
ECCB 2014 Accepted Posters with Abstracts
F: Evolution and population genomics
F03: Corinne Rancurel, Martine Da Rocha and Etienne G J Danchin.
Alienness: Rapid detection of horizontal gene transfers in metazoan genomes
Abstract:
Horizontal gene transfer (HGT) is the transmission of genetic material between species by ways other than
direct (vertical) inheritance from parents to the offspring. HGT is recognized as a major evolutionary force in
prokaryotes as it is involved in acquisition of antibiotic resistance or pathogeny. HGT has long been
overlooked and considered insignificant in eukaryotes. However, HGT have also played important roles in
the evolutionary history and biology of these species, including animals. For example, HGT have contributed
to the colonization of land by plants, in the emergence of plant parasitism in nematodes or in the
development of capabilities like resistance to extreme temperatures or desiccation. Progress in genome
sequencing technologies has allowed multiple animal genomes to be publicly released. Systematic searches
for HGT events in the root-knot nematodes or in the bdeloid rotifer, have shown that between 3 and 9 % of
protein-coding genes in these species were of foreign origin (1). However, in the absence of a user-friendly,
rapid and publicly available tool to detect HGT events in metazoan genomes, we still lack a global view of the
prevalence of HGT in animals.
Here, we propose a tool that allows automatic detection of putative HGT events, based on the predicted
protein set from a genome or transcriptome. Our tool has been specifically designed to rapidly detect genes
of non-metazoan origin (e.g. bacterial, fungal) in metazoan genomes (e.g. insects, mammals, nematodes).
Based on a blastP search against the NCBI's non-redundant library (nr), we retrieve putative homologs for
each protein query in a whole proteome. Canonical metazoan proteins should return better blast hits to
metazoans than to non-metazoans. Conversely, candidate HGT of non-metazoan origin are expected to
return better blast hits to non-metazoans than metazoans.
Our method uses the Alien Index metrics as described in (2) to detect a significant gap between the best
metazoan and non-metazoan e-values as an indicator of putative HGT. An Alien Index (AI) > 0, indicates a
better hit to non-metazoans than to metazoans. An AI > 30 corresponds to a difference of magnitude > e10
between the best non-metazoan and metazoan e-values and is estimated to be a clear indication of HGT.
The main difficulty of this approach is to automatically retrieve taxonomic information and to assign a hit to
either metazoan, or non-metazoan categories. Our methods not only allows classifying best blast hits in
metazoans and non-metazoans but it further classifies non-metazoan best hits into virus, bacteria, archaea,
fungi, plant and "other". Thus it allows both the detection of putative HGT acquisitions and identification of
the putative donors.
References
1. J.-F. Flot et al., Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga, Nature (2013).
2. E. A. Gladyshev, et al., Massive horizontal gene transfer in bdelloid rotifers, Science (2008).
Example of detected HGT
Gene : cds.comp59722_c0_seq1
Best non-metazoan e-value : 7.0e
-153
(bacterium)
Best metazon e-value: 7.0e
-42
AI = 255.6
Pfam : Glyco_hydro_32N
Putative function: invertase
Recording the best metazoan and non-metazoan e-values
Rapid detection of horizontal gene transfers in metazoan genomes
Corinne Rancurel
1
, Martine Da Rocha
1
, Etienne G J Danchin
1
Abstract : Horizontal gene transfer (HGT) is the transmission of
genetic material between species by ways other than direct (vertical)
inheritance from parents to the offspring. HGT is recognized as a major
evolutionary force in prokaryotes as it is involved in acquisition of
antibiotic resistance or pathogeny. HGT has long been overlooked and
considered insignificant in eukaryotes. However, HGT have also played
important roles in the evolutionary history and biology of these species,
including animals.
Our pipeline allows rapid detection of potential HGT of non metazoan
origin (e.g. bacteria, fungi, plant, protists) in metazoan genomes (e.g.
insects, vertebrates, nematodes , cnidaria).
Archeae
Reptiles
Echinoderms
Mollusks
Bacteria
Cnidaria
Mammals
Plants
Annelids
Porifera
Insects
Nematodes
Fungi
Red algae
Vertebrates
Bilateria
Eukaryotes
Vertical transmission
from parents to the offsrping
Metazoa
M
METAZOA
NON-METAZOA
HGT from non metazoa to metazoa
Alien index (AI) = log ((best e-value for Metazoan)+ e
-200
) – log ((best e-value for Non-Metazoan)+ e
-200
)
in our example : log (2e
-24
+ e
-200
) – log (1e
-37
+ e
-200
) = +30,6
Recording of the
best:
Metazoan &
Non Metazoan
e-values, for each
query
Non Redondant
NCBI library
NR
LINEAGE
Taxonomic
NCBI files
HITS
BLASTP
Compute
Alien Index AI
by query
[1]
Alien Index by
query (xls)
Select Input File
Query proteome (fasta)
Output Blast Hits (tabular)
Fill option
Exclude_group
[1]
[2]
[3]
Identification of potentiel
horizontal gene transfers
[2]
[3]
1
INRA UMR1355, UNS, CNRS UMR7254, F-06903, Sophia Antipolis, France. spiboc.bioinfo@sophia.inra.fr
Alienness
Rapid detection o
horizontal
ene trans
ers in metazoan
enome
C
orinne Rancurel
1
, Martine
D
a
Rocha
1
, Etienne
G
J
D
anchi
n
1
1
INRA UMR1355
, U
NS,
C
NR
S
UMR725
4,
F
-
0
6903,
S
o
phi
a Anti
pol
is, France.
spi
boc.bioin
fo@
sop
hia.inra.
f
r
[ref. Massive Horizontal gene Transfer in Bdelloid Rotifers , Gladyshev et al. Science 2008 ]
# BLASTP 2.2.26+
# Query: ANUcomp28394_c0_seq1
# Database: nr
# Fields: query id, subject id, % identity, …. evalue, bit score, subject ids
# 250 hits found
ANUcomp28394_c0_seq1 gi|522006232 40.98 …. 1e-37 144
………
ANUcomp28394_c0_seq1 gi|110671508 33.52 …. 2e-24 105
Tabular blast output
2
1
1
2
ComputeAlien Index
An AI is calculated for each query protein returning at least one hit either to a metazoan or a non-metazoan species
using the following formula :
3
3
NB : When no metazoan or non-metazoan significant BLAST hit is found, an e-value of 1 is automatically assigned as
the best metazoan or non-metazoanhit, respectively.
Rules Meaning Decision
AI > 0 e-value non-metazoan > evalue metazoan possible HGT event
AI > 30 corresponds to a difference of magnitude e
10
(see example) indicative of a HGT event
AI > 0 and
% identity > 70
strong presumption of contamination not considered as HGT event
Examples of results obtained withAlienness:
1
122
0
1
12
231
203
Archaea
Bacteria
Viroids
Viruses
Viridiplantae
Fungi
Other
Putative donors
Validation of HGT via phylogeny
0.4
1
1
1
0,9792
1
1
1
1
1
1
0,9583
1
1
1
0,9583
1
0,875
0,9792
1
1
1
1
1
1
0,75
1
0,9167
1
1
1
1
0,5208
0,7292
0,9583
1
1
1
1
1
1
1
1
1
1
1
0,8542
0,9792
1
0,875
1
1
1
1
1
1
1
0,8958
1
1
1
1
1
1
1
1
0,9167
1
1
1
95
1
99
1
100
1
100
1
91
Plant-parasitic Nematodes (Tylenchida)
Rhizobial bacteria
INSECT
Other bacteria
N. aberrans
1
1
0,9583
1
[ref. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary
endoparasitism in plant-parasitic nematodes, Eves-van den Akkeret al. GBE 2014 ]
BLAST hits are parsed to retrieve
associated taxonomic information from
the NCBI. Self-hits are ignored by
indicating the NCBI taxonomic
identifier of the query organism in the
(exclude_group option). The same
option can be used to ignore the
whole parent lineage.
For example, one can be interested by HGT of non-metazoan origin in the human
genome specifically (taxid = 9606) , or in the whole primate lineage (taxid = 9443),
in both case, using the human proteome as a query.
catarrhini
humans
chimpanzees
gorillas
gibbons
platyrrhini
old world monkey
new world monkey
anthropoids
prosimians
primates
lemurs, lorises
hominoidea
Query proteome : the plant-parasitic nematode Nacobbus aberrans (clade Tylenchida)
Exclude group : Tylenchida (Taxid: 6300)
Results : 570 N. aberrans proteins returned an Alien Index (AI) >30
and less than 70 % identity to a non-metazoan protein
Conclusion and Perspectives
14 query proteomes have been analyzedso far
Automatically generate functional annotationand eliminate contamination
Generating automatic phylogenies
Bacteria
Eukarya
Archaea
Virus
[ ref. D.Raoult. The post-Darwinist rhizome of life. The Lancet. 2010 ]
ResearchGate has not been able to resolve any citations for this publication.
Article
Full-text available
Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
Article
Full-text available
Horizontal gene transfer in metazoans has been documented in only a few species and is usually associated with endosymbiosis or parasitism. By contrast, in bdelloid rotifers we found many genes that appear to have originated in bacteria, fungi, and plants, concentrated in telomeric regions along with diverse mobile genetic elements. Bdelloid proximal gene-rich regions, however, appeared to lack foreign genes, thereby resembling those of model metazoan organisms. Some of the foreign genes were defective, whereas others were intact and transcribed; some of the latter contained functional spliceosomal introns. One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution.
Massive horizontal gene transfer in bdelloid rotifers Example of detected HGT Gene : cds.comp59722_c0_seq1 Best non-metazoan e-value : 7.0e -153 (bacterium) Best metazon e-value: 7
  • E A Gladyshev
E. A. Gladyshev, et al., Massive horizontal gene transfer in bdelloid rotifers, Science (2008). Example of detected HGT Gene : cds.comp59722_c0_seq1 Best non-metazoan e-value : 7.0e -153 (bacterium) Best metazon e-value: 7.0e -42 AI = 255.6