Phylogenomics of tomato chloroplasts using assembly and alignment-free method.
Identifieur interne : 000862 ( Main/Exploration ); précédent : 000861; suivant : 000863Phylogenomics of tomato chloroplasts using assembly and alignment-free method.
Auteurs : Raúl Martin Amado Cattáneo [Argentine] ; Luis Diambra [Argentine] ; Andrés Norman Mccarthy [Argentine]Source :
- Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis [ 2470-1408 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Chloroplast.
- classification : Lycopersicon esculentum.
- genetics : Lycopersicon esculentum.
- methods : DNA Barcoding, Taxonomic, Sequence Alignment.
- standards : DNA Barcoding, Taxonomic, Sequence Alignment.
- Phylogeny.
Abstract
Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.
DOI: 10.1080/24701394.2017.1419214
PubMed: 29338473
Affiliations:
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Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filtered out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.</div></front></TEI><affiliations><list><country><li>Argentine</li></country></list><tree><country name="Argentine"><noRegion><name sortKey="Amado Cattaneo, Raul Martin" sort="Amado Cattaneo, Raul Martin" uniqKey="Amado Cattaneo R" first="Raúl Martin" last="Amado Cattáneo">Raúl Martin Amado Cattáneo</name></noRegion><name sortKey="Diambra, Luis" sort="Diambra, Luis" uniqKey="Diambra L" first="Luis" last="Diambra">Luis Diambra</name><name sortKey="Mccarthy, Andres Norman" sort="Mccarthy, Andres Norman" uniqKey="Mccarthy A" first="Andrés Norman" last="Mccarthy">Andrés Norman Mccarthy</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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