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Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case

Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample ide...

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Autores principales: Xu, Tao, Kong, Lingfeng, Li, Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9318368/
https://www.ncbi.nlm.nih.gov/pubmed/35885975
http://dx.doi.org/10.3390/genes13071192
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author Xu, Tao
Kong, Lingfeng
Li, Qi
author_facet Xu, Tao
Kong, Lingfeng
Li, Qi
author_sort Xu, Tao
collection PubMed
description Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims.
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spelling pubmed-93183682022-07-27 Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case Xu, Tao Kong, Lingfeng Li, Qi Genes (Basel) Article Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims. MDPI 2022-07-02 /pmc/articles/PMC9318368/ /pubmed/35885975 http://dx.doi.org/10.3390/genes13071192 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xu, Tao
Kong, Lingfeng
Li, Qi
Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title_full Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title_fullStr Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title_full_unstemmed Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title_short Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
title_sort testing efficacy of assembly-free and alignment-free methods for species identification using genome skims, with patellogastropoda as a test case
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9318368/
https://www.ncbi.nlm.nih.gov/pubmed/35885975
http://dx.doi.org/10.3390/genes13071192
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