Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 595-604 ◽  
Author(s):  
Ana Insua ◽  
María J López-Piñón ◽  
Ruth Freire ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Aequipecten Opercularis

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209–276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270–294 bp) and GC content ranged between 47 and 50% (ITS1, 43–49%; 5.8S rRNA gene, 56–57%; ITS2, 44–49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.Key words: scallops, Pectinidae, ribosomal DNA, internal transcribed spacers, phylogeny.

Genetic variation within the genus Macropostrongyloides (Nematoda: Strongyloidea) from Australian macropodid and vombatid marsupials

Parasitology ◽  
2019 ◽  
Vol 146 (13) ◽  
pp. 1673-1682 ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Neil B. Chilton ◽  
Abdul Jabbar
Keyword(s):  
Genetic Variation ◽  
Genetic Divergence ◽  
Species Complex ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rrna Gene ◽  
Similar Species ◽  
Geographical Regions

AbstractThe genetic variation and taxonomic status of the four morphologically-defined species of Macropostrongyloides in Australian macropodid and vombatid marsupials were examined using sequence data of the ITS+ region (=first and second internal transcribed spacers, and the 5.8S rRNA gene) of the nuclear ribosomal DNA. The results of the phylogenetic analyses revealed that Ma. baylisi was a species complex consisting of four genetically distinct groups, some of which are host-specific. In addition, Ma. lasiorhini in the common wombat (Vombatus ursinus) did not form a monophyletic clade with Ma. lasiorhini from the southern hairy-nosed wombat (Lasiorhinus latifrons), suggesting the possibility of cryptic (genetically distinct but morphologically similar) species. There was also some genetic divergence between Ma. dissimilis in swamp wallabies (Wallabia bicolor) from different geographical regions. In contrast, there was no genetic divergence among specimens of Ma. yamagutii across its broad geographical range or between host species (i.e. Macropus fuliginosus and M. giganteus). Macropostrongyloides dissimilis represented the sister taxon to Ma. baylisi, Ma. yamagutii and Ma. lasiorhini. Further morphological and molecular studies are required to assess the species complex of Ma. baylisi.

scholarly journals Resolving Tiarosporella spp. allied to Botryosphaeriaceae and Phacidiaceae

Phytotaxa ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 73 ◽  
Author(s):  
PEDRO W. Crous ◽  
Michael M. Müller ◽  
Romina M. Sánchez ◽  
Lucrecia Giordano ◽  
M. Virginia Bianchinotti ◽  
...  
Keyword(s):  
South Africa ◽  
Ribosomal Rna ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Large Subunit ◽  
Elongation Factor ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
New Taxon ◽  
5.8S Rrna Gene

The type species of the genus Tiarosporella, T. paludosa, is epitypified and confirmed as a member of the Botryosphaeriaceae. Based on morphology and DNA sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers (ITS) and 5.8S rRNA gene of the nrDNA operon, the genus Tiarosporella is shown to be poly- and paraphyletic. A group of isolates morphologically similar to T. paludosa cluster to the Phacidiaceae (Phacidiales, Leotiomycetes) and we accommodated them in Darkera, a genus associated with needle diseases of conifers, with D. picea introduced as a novel taxon. This new taxon includes isolates occurring on needles of Picea spp. in Europe (Finland, Norway and Switzerland) and differs from D. parca according to a five-locus alignment consisting of ITS, LSU, partial 18S nuclear ribosomal RNA, translation elongation factor 1-alpha and beta-tubulin genes. Four novel genera are introduced for tiarosporella-like fungi, namely Eutiarosporella based on E. tritici on Triticum aestivum from South Africa, Marasasiomyces based on M. karoo on Eriocephalus sp. from South Africa, Mucoharknessia based on M. cortaderiae on Cortaderia selloana from Argentina, and Sakireeta based on S. madreeya on Aristida setacea from India. Together with the genus Botryobambusa, these genera represent a subclade in the Botryosphaeriaceae that is ecologically diverse, occurring on Poaceae, as well as woody hosts, including endophytes, saprobes, and plant pathogens.

Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences

2005 ◽  
Vol 83 (5) ◽  
pp. 467-483 ◽  
Author(s):  
Suzanne I Warwick ◽  
Connie A Sauder
Keyword(s):  
Restriction Site ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Trnl Intron ◽  
Rrna Gene ◽  
Cpdna Sequence ◽  
Polymorphism Data ◽  
Restriction Site Polymorphisms

Using sequence data from the ITS region (internal transcribed spacers ITS-1 and ITS-2 of nuclear DNA and the 5.8 rRNA gene), chloroplast DNA (cpDNA) sequence data from the trnL intron, and cpDNA restriction site polymorphism data, we examined the evolutionary relationships of the tribe Brassiceae (Brassicaceae). A group of approximately 50 genera, it is distinguished by the presence of conduplicate cotyledons and (or) heteroarthrocarpic fruit. cpDNA restriction site data and ITS, trnL, and combined ITS/trnL sequence data were obtained for 22, 104, 94, and 87 taxa in the tribe, respectively. Results from maximum parsimony analyses of the cpDNA and ITS and ITS/trnL sequence data showed a monophyletic origin for the tribe, with the inclusion of controversial members Calepina, Conringia, and Orychophragmus. ITS- and ITS/trnL-based clades corresponded to taxonomic subtribes: Vellinae, Zillinae, and Savignyinae; but as with previous cpDNA studies, there was little support for subtribes Brassicinae, Raphaninae, and Moricandiinae. Although there was no support for the Rapa/Oleracea or Nigra cpDNA lineages, many cpDNA subclades within each of them were evident in the ITS- and ITS/trnL-based phylogeny. The trnL sequence data provided little or no resolution of tribal or subtribal limits. The ITS data indicated polyphyletic origins for Brassica, Diplotaxis, and Erucastrum.Key words: Brassiceae, Calepina, Conringia, Orychophragmus, ITS, trnL, cpDNA restriction site polymorphisms.

scholarly journals Molecular authentication of Euphorbia schimperiana Scheele using internal transcribed spacer sequences of nuclear ribosomal DNA

2021 ◽  
Vol 28 (1) ◽  
pp. 125-130
Author(s):  
Mesfer M Alqahtani ◽  
M Ajmal Ali ◽  
M Oliur Rahman ◽  
Fahad M Al Hemaid ◽  
Sidanand V Kambhar ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Important Species ◽  
Discrimination Ability ◽  
Plant Taxon

The Internal Transcribed Spacers (ITS) sequences of nuclear ribosomal DNA (nrDNA) are commonly used in plant molecular phylogenetics for the molecular based taxonomic identification and DNA barcoding because of shorter length and easy to amplify by using the universal primers, and further has discrimination ability to distinguish the taxon at lower taxonomic level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved medicinally important species Euphorbia schimperiana Scheele of the family Euphorbiaceae reported from Saudi Arabia. The combined length of the entire ITS region in E. schimperiana is 644 nucleotides. The study reveals that E. schimperiana shows a close proximity with the members of the subgenus Esula. Bangladesh J. Plant Taxon. 28(1): 125-130, 2021 (June)

Genetic analysis of pathogenic and nonpathogenic Fusarium oxysporum from tomato plants

2002 ◽  
Vol 80 (3) ◽  
pp. 271-279 ◽  
Author(s):  
Jian R Bao ◽  
Deborah R Fravel ◽  
Nichole R O'Neill ◽  
George Lazarovits ◽  
Peter van Berkum
Keyword(s):  
Genetic Diversity ◽  
Fusarium Oxysporum ◽  
Geographic Origin ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Aflp Data ◽  
5.8S Rrna Gene ◽  
Rdna Its ◽  
Wide Range

Forty-three Fusarium oxysporum strains and one Fusarium solani strain were analyzed for genetic diversity. These strains represent a wide range of geographic locations and were collected primarily from tomato (Lycopersicon esculentum) roots. Among all 43 F. oxysporum strains, 21 were not pathogenic to tomato, 20 were pathogenic, including 13 strains of Fusarium oxysporum lycopersici and seven strains of Fusarium oxysporum radicis-lycopersici, and two were other formae speciales of the fungus. Genetic diversity of all 43 strains was assessed by vegetative compatibility group (VCG), sequence analysis of the rDNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene, and amplified fragment length polymorphism (AFLP). Most of the F. o. lycopersici strains were assigned to VCG 0030, while most nonpathogenic ones were incompatible with each other. ITS region analysis grouped the strains into four clusters. The nonpathogenic F. oxysporum strains were in two groups, while the pathogenic strains were placed in two different groups. Pathogenic and nonpathogenic strains were also separated into different clusters based on AFLP data, although some nonpathogenic strains grouped with pathogenic strains. The population of pathogenic strains was less diverse than that of the nonpathogenic strains, suggesting that the pathogenic strains were possibly of monophyletic origin. For both pathogenic and nonpathogenic F. oxysporum strains, no relationship was observed between the genetic profiles and geographic origin; this may indicate that pathogens did not originate independently at each locality.Key words: Fusarium oxysporum, VCG, rDNA (ITS) sequence, AFLP.

Phylogenetic relationships of three tribes of cloacinine nematodes (Strongylida: Chabertiidae) from macropodid marsupials

2018 ◽  
Vol 93 (04) ◽  
pp. 486-493 ◽  
Author(s):  
N.B. Chilton ◽  
F. Huby-Chilton ◽  
A. Koehler ◽  
R.B. Gasser ◽  
I. Beveridge
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Host Genus ◽  
Single Host

AbstractThe phylogenetic relationships of 42 species of cloacinine nematodes belonging to three tribes (Coronostrongylinea, Macropostrongylinea and Zoniolaiminea) were examined based on sequence data of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. All nematodes examined are parasites of Australian macropodid marsupials. None of the three nematode tribes was monophyletic. Paraphyly was also encountered in three genera: Papillostrongylus, Monilonema and Wallabinema. Species within the genus Thallostonema were limited to a single host genus (i.e. Thylogale), whereas species within the five principal genera (Coronostrongylus, Macropostrongylus, Popovastrongylus, Wallabinema and Zoniolaimus) were found to occur in multiple host genera. Potential modes of evolution among these nematodes are discussed.

Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae : Leguminosae) based on DNA sequences of the internal transcribed spacer region

2003 ◽  
Vol 16 (1) ◽  
pp. 19 ◽  
Author(s):  
Daniel J. Murphy ◽  
Joseph T. Miller ◽  
Randall J. Bayer ◽  
Pauline Y. Ladiges
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Dna Repeat ◽  
Outgroup Taxon

The largest monophyletic group within Acacia is subgenus Phyllodineae, with more than 950 predominately Australian species, the majority characterised by adult foliage consisting of phyllodes. Molecular sequence data from the internal transcribed spacers (ITS) of the nuclear ribosomal DNA repeat were used to investigate the monophyly of seven sections within the subgenus. A nested PCR approach was used to amplify the ITS region. Fifty-one species representative of all sections were sequenced together with one outgroup taxon Lysiloma divaricata (Ingeae).Phylogenetic parsimony analysis suggested that there are two main clades within Phyllodineae but that only one section, Lycopodiifoliae, is apparently monophyletic. In one of the main clades, Lycopodifoliae is related to some taxa in sections Alatae and Pulchellae and some members of section Phyllodineae. In the second main clade, sections Juliflorae, Plurinerves and Botrycephalae cluster with other members of section Phyllodineae. The two sections that are characterised by bipinnate foliage, Botrycephalae and Pulchellae, are nested within phyllodinous clades, indicating that at least two separate reversals to bipinnate leaves have occurred. Botrycephalae is paraphyletic with respect to taxa from section Phyllodineae that have single-nerved phyllodes and racemose inflorescences.

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