<i>cpn</i>60 barcode sequences accurately identify newly defined genera within the <i>Lactobacillaceae</i>

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Abstract

The cpn60 barcode sequence has been established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of “universal” PCR primers for amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus, and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with whole-genome-based phylogeny. Aligning or mapping full-length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode makes it a useful target for the detection and identification of lactobacilli, as defined by the latest taxonomic framework.

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Most cited references 47

Record: found
Abstract: found
Article: not found

Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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Record: found
Abstract: found
Article: not found

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

S Altschul (1997)

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

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Record: found
Abstract: found
Article: not found

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

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Author and article information

Journal

Title: Canadian Journal of Microbiology

Abbreviated Title: Can. J. Microbiol.

Publisher: Canadian Science Publishing

ISSN (Print): 0008-4166

ISSN (Electronic): 1480-3275

Publication date Created: June 2022

Publication date (Print): June 2022

Volume: 68

Issue: 6

Pages: 457-464

Affiliations

[1 ]Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada.

Article

DOI: 10.1139/cjm-2021-0296

PubMed ID: 35230911

SO-VID: 13fd464a-a1b1-41fd-8755-da273d4c773f

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http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining

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