bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P8. IDENTIFICATION OF NUMTS THROUGH NGS DATA
Vincent Branders 1,2* , Chedly Kastally 2 & Patrick Mardulyn 2 .
Machine Learning Group, Institute of Information and Communication Technologies, Electronics and Applied
Mathematics (ICTEAM), Université catholique de Louvain 1 ; Evolutionary Biology and Ecology, Université libre de
Bruxelles 2 . * vincent.branders@uclouvain.be
Numts are copies of mitochondrial DNA sequences that have been transferred into the nuclear genome. Due to their
similarity with mitochondrial DNA sequences, numts have led to many misinterpretations from overestimation of
diversity to wrong association between cystic fibrosis and mitochondrial genome variation. To avoid such bias induced
by numts, theses sequences have to be identified. Current methodologies are based on comparisons of existing nuclear
and mitochondrial sequences and searches for similarities. The Pacific Biosciences (PacBio) new technology generates
sequencing reads that span thousands of base pairs, which gives the opportunity to identify numts by looking for reads
with regions similar to mitochondrial sequences and surrounded by regions highly different from it. It should allow the
systematic identification of numts without a complete known nuclear reference.
INTRODUCTION
The transfer of DNA from mitochondria to the nucleus
generates nuclear copies of mitochondrial DNA (numts).
Numts have been found in many species including yeasts,
rodents and plants. Due to their similarity to mitochondrial
DNA, numts are responsible for many misinterpretations,
both in mitochondrial disease studies and phylogenetic
reconstructions (Hazkani-Covo et al., 2010). Numt
variation have commonly been misreported as
mitochondrial mutations in patients (Yao et al., 2008).
Moreover, DNA barcoding was found to overestimate the
number of species when numts are coamplified (Song et
al., 2008). Current methods identify such sequences by
aligning mitochondrial sequences against the nuclear
genome and identifying similar regions (Figure 1, left).
The PacBio technology allows the sequencing of DNA
fragments spanning thousands of bases pairs. This size
should allow the identification of numts without the need
of a complete nuclear reference (the insect species
Gonioctena intermedia for example). Indeed, it should be
possible to use a mitochondrial assembly to identify
PacBio reads with a central region similar to the
mitochondrial sequence enclosed by nuclear regions that
are dissimilar to it (Figure 1, right).
FIGURE 1. Identification of numts – Existing methods (left) and proposed
method (right). Comparison of mitochondrial sequence to nuclear
sequence (left) or long reads (right).
METHODS
The proposed approach aligns PacBio reads to a
mitochondrial genome (here de novo assemblies of PacBio
reads and Illumina HiSeq 2000 reads are used). In these
long reads, numts are identified with one region similar
to the mitochondrial genome but surrounded by regions
that are not similar. We introduce different criteria to
distinguish reads that are presumably numts and reads of
mitochondrial origin (Figure 2). DNA sequences comes
from an insect (Gonioctena intermedia) without reference
genome.
FIGURE 2. Mitochondrial reads and numts with nuclear borders.
RESULTS & DISCUSSION
A systematic identification of potential numts is proposed:
through alignments, we identify 10 mitochondrial reads
and 34 reads with potential numt for one particular
mitochondrial region (the widely studied cytochrome
oxidase I gene). As an exploratory research, we highlight
the usefulness of Pacific Biosciences data in the
identification of numts when no nuclear reference is
available. It only requires PacBio reads and a
mitochondrial assembly. The proposed approach is more
efficient than an identification of numts through short
reads that would require the complete reconstruction of
both mitochondrial and nuclear genomes. A systematic
identification of numts in non-models organisms should
avoid misinterpretations in studies where numts could be
sources of bias. Our current distinction of numts and
mitochondrial reads is quite simple. A detailed analysis of
this distinction could be a perspective of improvements.
REFERENCES
Hazkani-Covo E. et al. PLOS Genetics 6, 1-11 (2010).
Song H. et al. PNAS 105, 13486-13491 (2008).
Yao Y. G. et al. Journal of Medical Genetics 45, 769-772 (2008).
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