bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P14. NOVOPLASTY: IN SILICO ASSEMBLY OF PLASTID GENOMES FROM
WHOLE GENOME NGS DATA
Nicolas Dierckxsens 1,2* , Olivier Hardy 2 , Ludwig Triest 3 , Patrick Mardulyn 2 & Guillaume Smits 1,4 .
Interuniversity Institute of Bioinformatics Brussels (IB2), ULB-VUB, Triomflaan CP 263, 1050 Brussels, Belgium 1 ;
Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. D.
Roosevelt 50, B-1050 Brussels, Belgium 2 ; Plant Biology and Nature Management, Vrije Universiteit Brussel, Brussels,
Belgium 3 ; Department of Paediatrics, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université Libre de
Bruxelles (ULB), Brussels, Belgium 4 . * nicolasdierckxsens@hotmail.com
Thanks to the evolution in next-generation sequencer (NGS) technology, whole genome data can be readily obtained
from a variety of samples. There are many algorithms available to assemble these reads, but few of them focus on
assembling the plastid genomes. Therefore we developed a new algorithm that solely assembles the plastid genomes
from whole genome data, starting from a single seed. The algorithm is capable of utilizing the full advantage of very high
coverage, which makes it even capable of assembling through problematic regions (AT-rich). The algorithm has been
tested on several whole genome Illumina datasets and it outperformed other assemblers in runtime and specificity. Every
assembly resulted in a single contig for any chloroplast or mitochondrial genome and this always within a timeframe of
30 minutes.
INTRODUCTION
Chloroplasts and mitochondria are both responsible for
generating metabolic energy within eukaryotic cells. Both
plastids are maternally inherited and have a persistent gene
organization, what makes them ideal for phylogenetic
studies or as a barcode in plant and food identification
(Brozynska et al., 2014). But assembling these plastids
genomes is not always that straightforward with the
currently available tools. Therefore we developed a new
algorithm, specifically for the assembly of plastid
genomes from whole genome data.
METHODS
The algorithm is written in Perl. All assemblies were
executed on Intel Xeon CPU machine containing 24 cores
of 2.93 GHz with a total of 96,8 GB of RAM. All nonhuman
samples were sequenced on the Illumina HiSeq
platform (101 bp paired-end reads). The human
mitochondria samples (PCR-free) were sequenced on the
Illumina HiSeqX platform (150 bp paired-end reads). The
Gonioctena intermedia sample was also sequenced on the
PacBio platform.
RESULTS & DISCUSSION
Algorithm. The algorithm is similar to string overlap
algorithms like SSAKE (Warren et al., 2007) and VCAKE
(Jeck et al., 2007). It starts with reading the sequences into
a hash table, which facilitates a quick accessibility. The
assembly has to be initiated by a seed that will be
extended bidirectionally in iterations. The seed input is
quite flexible, it can be one sequence read, a conserved
gene or even a complete mitochondrial genome from a
distant species. Every base extension is determined by a
consensus between the overlapping reads. Unlike most
assemblers, NOVOPlasty doesn’t try to assemble every
read, but will extend the given seed until the circular
plastid is formed.
Assemblies. NOVOPlasty has currently been tested for the
assembly of 8 chloroplasts and 6 mitochondria. Since
chloroplasts contain an inverted repeat, two versions of the
assembly are generated. The differ only in the orientation
of the region between the two repeats; the correct one will
have to be resolved manually. Besides the mitochondrion
of the leaf beetle Gonioctena intermedia, all assemblies
resulted in a complete circular genome. A comparative
study of four assemblers for the mitochondrial genome of
G. intermedia clearly shows the speed and specificity of
NOVOPlasty (Table 1).
NOVO
Plasty
MIRA MITO bim ARC
Duration (min) 12 536 4777* 586
Memory (GB) 15 57,6 63,4 1,9
Storage (GB) 0 144 418 12
Total contigs 1 3434 2221 2502
Mitochondrial contigs 1 1 4 48
Coverage (%) 98 94 94 84
Mismatches 10 25 26 2
Unidentified nucleotides 43 194 197 0
TABLE 1. Benchmarking results between four assemblies of the
mitochondrial genome of Gonioctena intermedia. The assemblies were
constructed with MITObim (Hahn et al., 2013), MIRA (Chevreux et al.,
1999), ARC (Hunter et al., 2015) and NOVOPlasty.*manually terminated
Discussion. Despite the many available assemblers, many
researchers still struggle to find a good assembler for
plastids genomes. NOVOPlasty offers an assembler
specifically designed for plastids that will deliver the
complete genome within 30 minutes. The algorithm will
be tested on more datasets and a comparative study with
other assemblers is in progress.
REFERENCES
Brozynska et al. PLoS One 9 (2014).
Chevreux et al. Computer Science and Biology: Proceedings of the
German Conference on Bioinformatics (GCB) (1999).
Hahn et al. Nucleic Acids Research, 1-9 (2013).
Hunter et al. http://dx.doi.org/10.1101/014662 (2015).
Jeck et al. BMC Bioinformatics 23, 2942-2944 (2007).
Warren et al. BMC Bioinformatics 23, 500-501 (2007).
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