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

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.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3120 ◽  
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.

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

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.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

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

2021 ◽  
pp. 124-130
Author(s):  
Anna D. Temraleeva ◽  
Elena S. Krivina ◽  
Yury S. Bukin
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequencing ◽  
Dna Barcoding ◽  
Species Identification ◽  
Green Algae ◽  
Molecular Genetic ◽  
Algal Species ◽  
Species Boundaries ◽  
Sequencing Technology ◽  
Dna Taxonomy

The understanding of the impossibility of distinguishing algal species based on morphological features came with the development of DNA sequencing technology, which today is a necessary tool for defining species boundaries and testing traditional species concepts. The paper discusses popular approaches to species identification (DNA barcoding) and the description of new and revision of known species (DNA taxonomy) using molecular genetic methods. The requirements and limitations in their work are given, as well as examples of phylogenetic analysis of green algae from the clade Moewusinia and Parachlorella, including the genus Micractinium.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

DNA barcoding of Antarctic marine zooplankton for species identification and recognition

2014 ◽  
Vol 24 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Fangping CHENG ◽  
Minxiao WANG ◽  
Song SUN ◽  
Chaolun LI ◽  
Yongshan ZHANG
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Marine Zooplankton ◽  
Antarctic Marine
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