The current approaches to the study of algae: DNA barcoding and DNA taxonomy

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’.

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Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology

10.1101/281048 ◽

2018 ◽

Cited By ~ 2

Author(s):

Joe Parker ◽

Andrew Helmstetter ◽

James Crowe ◽

John Iacona ◽

Dion Devey ◽

...

Keyword(s):

Dna Sequencing ◽

Species Identification ◽

Sequence Data ◽

Vascular Plant ◽

Reference Sequence ◽

Read Length ◽

Reference Database ◽

Sequencing Technology ◽

Long Read ◽

Suitable Reference

AbstractThe versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organism’s genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses.

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PHILOGENETIC DIVERSITY OF FUNGI OF THE GENUS PENICILLIUM AND TALAROMYCES ASSOCIATED WITH BROWN ALGAE OF THE GENUS SARGASSUM

EurasianUnionScientists ◽

10.31618/esu.2413-9335.2020.3.78.1011 ◽

2020 ◽

Vol 3 (9(78)) ◽

pp. 12-18

Author(s):

N. Kirichuk ◽

M. Pivkin ◽

Yu. Hudyakova

Keyword(s):

Phylogenetic Analysis ◽

Species Identification ◽

Sea Of Japan ◽

Brown Algae ◽

Phylogenetic Diversity ◽

Molecular Genetic ◽

The Sea Of Japan ◽

Gene Sequences ◽

Penicillium Species ◽

As Species

The results of the investigation of Penicillium sensu lato phylogenetic diversity of brown algae Sargassum spp. (the Sea of Japan) are presented in this article. Seventeen fungal strains were studied using traditional methods of phenotypic investigations and modern molecular-genetic approaches. As a result of phylogenetic analysis of ITS and BenA gene sequences, Penicillium species from five sections were revealed (sections Fasciculata, Paradoxa, Ramosa, Canescentia, Aspergilloides). One strain was identified as species of Talaromyces which more related to section Talaromyces. Five species (P. spinulosum, P. subspinulosum, P. roseomaculatum, P. thomii, P. murcianum, P. antarcticum) were identified based on BenA gene analysis. For species identification of some strains additional analysis of genetic and phenotypic features is necessary.

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Evaluating multi-locus phylogenies for species boundaries determination in the genusDiaporthe

PeerJ ◽

10.7717/peerj.3120 ◽

2017 ◽

Vol 5 ◽

pp. e3120 ◽

Cited By ~ 18

Author(s):

Liliana Santos ◽

Artur Alves ◽

Rui Alves

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Open Problem ◽

Phylogenetic Trees ◽

Species Boundaries ◽

Species Separation ◽

Phytosanitary Measures ◽

Optimal Set ◽

Disease Understanding

BackgroundSpecies identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genusDiaporthe. AccurateDiaporthespecies separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.MethodsHere we addressed that problem by identifying five loci that have been sequenced in 142Diaportheisolates representing 96 species:TEF1,TUB,CAL,HISand ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.ResultsAs expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying theTEF1-TUB-CAL-HIS4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.DiscussionOur results question the current use of the ITS locus for DNA barcoding in the genusDiaportheand suggest thatTEF1might be a better choice if one locus barcoding needs to be done.

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Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

10.7287/peerj.preprints.2822v1 ◽

2017 ◽

Author(s):

Liliana Santos ◽

Artur Alves ◽

Rui Alves

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Open Problem ◽

Phylogenetic Trees ◽

Species Boundaries ◽

Species Separation ◽

Phytosanitary Measures ◽

Optimal Set ◽

Disease Understanding

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

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Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

10.7287/peerj.preprints.2822 ◽

2017 ◽

Author(s):

Liliana Santos ◽

Artur Alves ◽

Rui Alves

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Open Problem ◽

Phylogenetic Trees ◽

Species Boundaries ◽

Species Separation ◽

Phytosanitary Measures ◽

Optimal Set ◽

Disease Understanding

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

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