Phylogenetic Relationship of Mangosteen (Garcinia mangostana) and Several Wild Relatives (Garcinia spp.) Revealed by ITS Sequence Data

The phylogenetic relationships among 17 Garcinia species including G. mangostana (mangosteen) were analyzed by comparing sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). Both parsimonious and neighbor joining (NJ) analyses revealed that G. mangostana is closely related to G. malaccensis believed to be a progenitor of mangosteen. Another suspected progenitor of mangosteen, G. hombroniana, was more distant from G. mangostana than G. malaccensis phylogenetically. Garcinia hombroniana formed a cluster with G. rostrata, G, speciosa and G. sizygiifolia, and this cluster was connected with a cluster of G. mangostana and G. malaccensis. The ITS sequence analysis showed that G. atroviridis, G. cowa, G. dulcis, G. malaccensis, G. mangostana, G. rostrata and G. vilersiana have nucleotide additivity (two different nucleotides at the same nucleotide position) at several sites in the ITS region. The occurrence of these species might be related to hybridization with ancestors, but the genomic compositions, even chromosome numbers, of these species are still unknown.

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Higher-level relationships among the eucalypts are resolved by ITS-sequence data

Australian Systematic Botany ◽

10.1071/sb00039 ◽

2002 ◽

Vol 15 (1) ◽

pp. 49 ◽

Cited By ~ 82

Author(s):

Dorothy A. Steane ◽

Dean Nicolle ◽

Gay E. McKinnon ◽

René E. Vaillancourt ◽

Brad M. Potts

Keyword(s):

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

Its Sequence ◽

Phylogenetic Groups ◽

Single Section ◽

Western Australian ◽

Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

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Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

Canadian Journal of Botany ◽

10.1139/b05-161 ◽

2006 ◽

Vol 84 (2) ◽

pp. 269-281 ◽

Cited By ~ 33

Author(s):

Suzanne I. Warwick ◽

Ihsan A. Al-Shehbaz ◽

Connie A. Sauder

Keyword(s):

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Molecular Data ◽

The Other ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Position ◽

New Combinations ◽

Arabidopsis Lyrata ◽

Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

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Comparison of the ITS Sequences of 5 Common Potentilla Species in Jilin Province of China

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.554-556.1690 ◽

2012 ◽

Vol 554-556 ◽

pp. 1690-1693 ◽

Cited By ~ 2

Author(s):

Shao Xuan Zhang ◽

Xin Rui Liu ◽

Bo Chuan Wang ◽

Yun Hui Ling ◽

De Jun Sun ◽

...

Keyword(s):

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Scientific Data ◽

Jilin Province ◽

Its Sequences ◽

Universal Primers ◽

Its Sequence ◽

Its Sequence Analysis ◽

Pcr Products

To find the differences in the internal transcribed spacer(ITS) sequences and provide scientific data for the authentication of Potentilla chinensis and its related species, we extracted the genome DNA from the leaves of 5 common Potetilla species in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. Polymorphism of ITS sequences was found within P. chinensis and the sequence data suggested that our samples of this species might be related to hybridization. Other 4 species showed intraspecies-stability in ITS sequence. The ITS sequences of these 5 Potentilla species are significantly different. So ITS sequence analysis and other methods derived from it can be used in authentication of Potentilla.

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Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

10.21203/rs.2.14347/v3 ◽

2019 ◽

Author(s):

Michael Bradshaw ◽

Felix Grewe ◽

Anne Thomas ◽

Cody H. Harrison ◽

Hanna Lindgren ◽

...

Keyword(s):

Species Complex ◽

High Throughput Sequencing ◽

Sequence Data ◽

Dna Barcode ◽

Intergenic Spacer ◽

Its Region ◽

Nuclear Ribosomal Dna ◽

Nucleotide Position ◽

Ribosomal Operon ◽

Intragenomic Variation

Abstract Background: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, IGS, and some intronic regions; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

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Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

10.21203/rs.2.14347/v1 ◽

2019 ◽

Author(s):

Michael Bradshaw ◽

Felix Grewe ◽

Anne Thomas ◽

Cody H. Harrison ◽

Hanna Lindgren ◽

...

Keyword(s):

Species Complex ◽

Sequence Data ◽

Dna Barcode ◽

Intergenic Spacer ◽

Its Region ◽

Nuclear Ribosomal Dna ◽

Nucleotide Position ◽

Phylogenetic Reconstructions ◽

Ribosomal Operon ◽

Intragenomic Variation

Abstract Background Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from approximate nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing.Results We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic reconstructions of the ITS, 28S, IGS, and some intronic regions; however, phylogenetic reconstructions based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed, previously unrecognized lineages in the nrDNA phylogeny.Conclusions The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited number of potentially polymorphic sites generally do not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution.

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Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

10.21203/rs.2.14347/v4 ◽

2019 ◽

Author(s):

Michael Bradshaw ◽

Felix Grewe ◽

Anne Thomas ◽

Cody H. Harrison ◽

Hanna Lindgren ◽

...

Keyword(s):

Species Complex ◽

High Throughput Sequencing ◽

Sequence Data ◽

Dna Barcode ◽

Intergenic Spacer ◽

Its Region ◽

Nuclear Ribosomal Dna ◽

Nucleotide Position ◽

Ribosomal Operon ◽

Intragenomic Variation

Abstract Background: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

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Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

BMC Evolutionary Biology ◽

10.1186/s12862-019-1571-4 ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Michael Bradshaw ◽

Felix Grewe ◽

Anne Thomas ◽

Cody H. Harrison ◽

Hanna Lindgren ◽

...

Keyword(s):

Species Complex ◽

High Throughput Sequencing ◽

Sequence Data ◽

Dna Barcode ◽

Intergenic Spacer ◽

Its Region ◽

Nuclear Ribosomal Dna ◽

Nucleotide Position ◽

Ribosomal Operon ◽

Intragenomic Variation

Abstract Background Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

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Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

10.21203/rs.2.14347/v2 ◽

2019 ◽

Author(s):

Michael Bradshaw ◽

Felix Grewe ◽

Anne Thomas ◽

Cody H. Harrison ◽

Hanna Lindgren ◽

...

Keyword(s):

Species Complex ◽

High Throughput Sequencing ◽

Sequence Data ◽

Dna Barcode ◽

Intergenic Spacer ◽

Its Region ◽

Nuclear Ribosomal Dna ◽

Nucleotide Position ◽

Ribosomal Operon ◽

Intragenomic Variation

Abstract Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, IGS, and some intronic regions; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

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WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

The Scientific World JOURNAL ◽

10.1100/2012/689296 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Victor Olusegun Oyetayo

Keyword(s):

Sequence Analysis ◽

Phylogenetic Tree ◽

Molecular Identification ◽

Internal Transcribed Spacer ◽

Its Region ◽

Its Sequence ◽

African Countries ◽

African Species ◽

Its Sequence Analysis ◽

Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

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