Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
Identifieur interne : 000C59 ( Main/Exploration ); précédent : 000C58; suivant : 000C60Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
Auteurs : Kosai Al-Nakeeb ; Thomas Nordahl Petersen ; Thomas Sicheritz-PonténSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Chloroplast, DNA, Mitochondrial.
- methods : Whole Genome Sequencing.
- Animals, Genome, Chloroplast, Genome, Mitochondrial, Software.
Abstract
Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling.
Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers.
Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at:
The online version of this article (doi:10.1186/s12859-017-1927-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-017-1927-y
PubMed: 29162031
PubMed Central: 5699183
Affiliations:
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Petersen</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Sicheritz Ponten, Thomas" sort="Sicheritz Ponten, Thomas" uniqKey="Sicheritz Ponten T" first="Thomas" last="Sicheritz-Pontén">Thomas Sicheritz-Pontén</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>DNA, Chloroplast (genetics)</term><term>DNA, Mitochondrial (genetics)</term><term>Genome, Chloroplast</term><term>Genome, Mitochondrial</term><term>Software</term><term>Whole Genome Sequencing (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des chloroplastes (génétique)</term><term>ADN mitochondrial (génétique)</term><term>Animaux</term><term>Génome de chloroplaste</term><term>Génome mitochondrial</term><term>Logiciel</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Chloroplast</term><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des chloroplastes</term><term>ADN mitochondrial</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Genome, Chloroplast</term><term>Genome, Mitochondrial</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Génome de chloroplaste</term><term>Génome mitochondrial</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling.</p></sec><sec><title>Results</title><p>Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers.</p></sec><sec><title>Conclusion</title><p>Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/kosaidtu/norgal">https://bitbucket.org/kosaidtu/norgal</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12859-017-1927-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bruggen, Efjv" uniqKey="Bruggen E">EFJV Bruggen</name></author><author><name sortKey="Borst, P" uniqKey="Borst P">P Borst</name></author><author><name sortKey="Ruttenberg, Gjcm" uniqKey="Ruttenberg G">GJCM Ruttenberg</name></author><author><name sortKey="Gruber, M" uniqKey="Gruber M">M Gruber</name></author><author><name sortKey="Kroon, Am" uniqKey="Kroon A">AM Kroon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hahn, C" uniqKey="Hahn C">C Hahn</name></author><author><name 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Dalén</name></author><author><name sortKey="Blom, N" uniqKey="Blom N">N Blom</name></author><author><name sortKey="Sicheritz Ponten, T" uniqKey="Sicheritz Ponten T">T Sicheritz-Pontén</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schubert, M" uniqKey="Schubert M">M Schubert</name></author><author><name sortKey="Lindgreen, S" uniqKey="Lindgreen S">S Lindgreen</name></author><author><name sortKey="Orlando, L" uniqKey="Orlando L">L Orlando</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Liu, Cm" uniqKey="Liu C">CM Liu</name></author><author><name sortKey="Luo, R" uniqKey="Luo R">R Luo</name></author><author><name sortKey="Sadakane, K" uniqKey="Sadakane K">K Sadakane</name></author><author><name sortKey="Lam, Tw" uniqKey="Lam T">TW Lam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H 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Al-Nakeeb</name><name sortKey="Petersen, Thomas Nordahl" sort="Petersen, Thomas Nordahl" uniqKey="Petersen T" first="Thomas Nordahl" last="Petersen">Thomas Nordahl Petersen</name><name sortKey="Sicheritz Ponten, Thomas" sort="Sicheritz Ponten, Thomas" uniqKey="Sicheritz Ponten T" first="Thomas" last="Sicheritz-Pontén">Thomas Sicheritz-Pontén</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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