Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings. Based on the K2P distance, significant divergences between the inter- and intraspecific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

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Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

PeerJ ◽

10.7717/peerj.2638 ◽

2016 ◽

Vol 4 ◽

pp. e2638 ◽

Cited By ~ 6

Author(s):

Priyanka Mishra ◽

Amit Kumar ◽

Vereena Rodrigues ◽

Ashutosh K. Shukla ◽

Velusamy Sundaresan

Keyword(s):

Dna Barcoding ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Its Region ◽

Genetic Distances ◽

Discrimination Power ◽

Distance Method ◽

Tree Reconciliation ◽

Its1 Region ◽

Barcoding Gap

Premise of the StudyThe internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the generaCassia, SennaandChamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.MethodologyA combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generatedsequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.Principal FindingsBased on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses.ConclusionThe reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

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Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

10.7287/peerj.preprints.2434v1 ◽

2016 ◽

Author(s):

Priyanka Mishra ◽

Amit Kumar ◽

Vereena Rodrigues ◽

Ashutosh K Shukla ◽

Velusamy Sundaesan

Keyword(s):

Dna Barcoding ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Its Region ◽

Genetic Distances ◽

Discrimination Power ◽

Distance Method ◽

Tree Reconciliation ◽

Its1 Region ◽

Barcoding Gap

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings. Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2 there by concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

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

PeerJ ◽

10.7717/peerj.4499 ◽

2018 ◽

Vol 6 ◽

pp. e4499 ◽

Cited By ~ 1

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.

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Single molecule, near full-length genome sequencing of dengue virus

Scientific Reports ◽

10.1038/s41598-020-75374-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Thiruni N. Adikari ◽

Nasir Riaz ◽

Chathurani Sigera ◽

Preston Leung ◽

Braulio M. Valencia ◽

...

Keyword(s):

Dengue Virus ◽

Single Molecule ◽

Phylogenetic Trees ◽

Sequence Data ◽

Sequence Similarity ◽

Genetic Distances ◽

Full Length ◽

Denv Serotypes ◽

Consensus Sequences ◽

Pairwise Sequence Similarity

Abstract Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process is laborious, costly and requires at least 10 primers per serotype, thus increasing the likelihood of PCR bias. We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation “nanopore” technology without fragmenting and use the sequence data to differentiate within-host viral variants with a bioinformatics tool (Nano-Q). The new assay successfully generated near full-length amplicons from DENV serotypes 1, 2 and 3 samples which were sequenced with nanopore technology. Consensus DENV sequences generated by nanopore sequencing had over 99.5% pairwise sequence similarity to Illumina generated counterparts provided the coverage was > 100 with both platforms. Maximum likelihood phylogenetic trees generated from nanopore consensus sequences were able to reproduce the exact trees made from Illumina sequencing with a conservative 99% bootstrapping threshold (after 1000 replicates and 10% burn-in). Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host.

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Molecular identification of common hard ticks (Acari: Ixodidae) in Xinjiang, China

Zootaxa ◽

10.11646/zootaxa.4950.1.2 ◽

2021 ◽

Vol 4950 (1) ◽

pp. 46-60

Author(s):

QIGUO WANG ◽

YUJIANG ZHANG ◽

SURONG SUN ◽

TAO LUO ◽

WENTING MOU ◽

...

Keyword(s):

16S Rdna ◽

Phylogenetic Trees ◽

Rhipicephalus Sanguineus ◽

Genetic Distances ◽

Neighbor Joining ◽

Minimum Evolution ◽

Rdna Genes ◽

Hard Ticks ◽

Distance Model ◽

Two Parameter

We provide data on the cytochrome c oxidase subunit I (COI) and 16S rDNA genes for eight species of common hard ticks in Xinjiang: Dermacentor montanus, D. niveus, Haemaphysalis sulcate, Hyalomma asiaticum asiaticum, Hya. detritum, Hya. scupense, Rhipicephalus sanguineus and R. pumilio. Genetic distances, calculated based on the Kimura two-parameter (K2P) distance model, found the same trend of intraspecies level≤interspecies level<intragenus level. Phylogenetic trees, constructed with the neighbor-joining (NJ) and minimum-evolution (ME) methods, demonstrated that each species clustered into separate clades, thus confirming the usefulness of CO1 and 16S rDNA genes for tick species identification. The genera Dermacentor, Haemaphysalis and Rhipicephalus were all recovered in the phylogenetic analysis, as was the subfamily Rhipicephalinae, but a monophyletic Hyalomma was not.

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

10.7287/peerj.preprints.26494 ◽

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.

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

10.7287/peerj.preprints.26494v1 ◽

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.

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Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences

Viruses ◽

10.3390/v13050764 ◽

2021 ◽

Vol 13 (5) ◽

pp. 764

Author(s):

Bohu Pan ◽

Zuowei Ji ◽

Sugunadevi Sakkiah ◽

Wenjing Guo ◽

Jie Liu ◽

...

Keyword(s):

Clustering Analysis ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Host Age ◽

Hierarchical Clustering Analysis ◽

Genome Sequences ◽

Geographic Patterns ◽

Rapid Spread ◽

Pairwise Sequence Similarity ◽

Sequence Similarity Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.

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Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.067405-0 ◽

2014 ◽

Vol 64 (Pt_12) ◽

pp. 4068-4072 ◽

Cited By ~ 7

Author(s):

Young-Ok Kim ◽

Sooyeon Park ◽

Doo Nam Kim ◽

Bo-Hye Nam ◽

Sung-Min Won ◽

...

Keyword(s):

Phylogenetic Trees ◽

Sequence Similarity ◽

Beluga Whale ◽

Delphinapterus Leucas ◽

Rrna Gene ◽

Phenotypic Properties ◽

Content Type ◽

Link Type ◽

Beluga Whale Delphinapterus Leucas ◽

Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1T, was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1T joins the cluster comprising the type strains of three species of the genus Amphritea , with which it exhibited 95.8–96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1T was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1T is separated from other species of the genus Amphritea . On the basis of the data presented, strain RA1T is considered to represent a novel species of the genus Amphritea , for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1T ( = KCTC 42154T = NBRC 110551T).

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