Estimating the total genome length of a metagenomic sample using k-mers
Identifieur interne : 000587 ( Main/Exploration ); précédent : 000586; suivant : 000588Estimating the total genome length of a metagenomic sample using k-mers
Auteurs : Kui Hua [République populaire de Chine] ; Xuegong Zhang [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Microbiota.
- methods : Metagenomics.
- Algorithms, Datasets as Topic, High-Throughput Nucleotide Sequencing, Humans, Metagenome, Sequence Analysis, DNA, Software.
Abstract
Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.
As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (
We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.
The online version of this article (10.1186/s12864-019-5467-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-019-5467-x
PubMed: 30967110
PubMed Central: 6456951
Affiliations:
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Center for Synthetic & System Biology, BNRIST,</institution></institution-wrap>Beijing, 100084 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0662 3178</institution-id><institution-id institution-id-type="GRID">grid.12527.33</institution-id><institution>Department of Automation, Tsinghua University,</institution></institution-wrap>Beijing, 100084 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Xuegong" sort="Zhang, Xuegong" uniqKey="Zhang X" first="Xuegong" last="Zhang">Xuegong Zhang</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0369 313X</institution-id><institution-id 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institution-id-type="GRID">grid.12527.33</institution-id><institution>School of Life Sciences, Tsinghua University,</institution></institution-wrap>Beijing, 100084 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Datasets as Topic</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Metagenome</term><term>Metagenomics (methods)</term><term>Microbiota (genetics)</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Données de la recherche comme sujet</term><term>Humains</term><term>Logiciel</term><term>Microbiote (génétique)</term><term>Métagénome</term><term>Métagénomique ()</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microbiota</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Microbiote</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Datasets as Topic</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Metagenome</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Données de la recherche comme sujet</term><term>Humains</term><term>Logiciel</term><term>Métagénome</term><term>Métagénomique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.</p></sec><sec><title>Results</title><p>As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (<italic>KRI</italic>) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses.</p></sec><sec><title>Conclusions</title><p>We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12864-019-5467-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gordon, Ji" uniqKey="Gordon J">JI Gordon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Falony, G" uniqKey="Falony G">G Falony</name></author><author><name sortKey="Wijmenga, C" uniqKey="Wijmenga C">C Wijmenga</name></author><author><name sortKey="Raes, J" uniqKey="Raes J">J 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Liggett C">CM Fraser-Liggett</name></author><author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name></author><author><name sortKey="Gordon, Ji" uniqKey="Gordon J">JI Gordon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author><author><name sortKey="Kristiansen, K" uniqKey="Kristiansen K">K Kristiansen</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Hua, Kui" sort="Hua, Kui" uniqKey="Hua K" first="Kui" last="Hua">Kui Hua</name></noRegion><name sortKey="Hua, Kui" sort="Hua, Kui" uniqKey="Hua K" first="Kui" last="Hua">Kui Hua</name><name sortKey="Zhang, Xuegong" sort="Zhang, Xuegong" uniqKey="Zhang X" first="Xuegong" last="Zhang">Xuegong Zhang</name><name sortKey="Zhang, Xuegong" sort="Zhang, Xuegong" uniqKey="Zhang X" first="Xuegong" last="Zhang">Xuegong Zhang</name><name sortKey="Zhang, Xuegong" sort="Zhang, Xuegong" uniqKey="Zhang X" first="Xuegong" last="Zhang">Xuegong Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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