Species relationships between antifungal chitinase and nuclear rDNA (internal transcribed spacer) sequences in the genus Hordeum

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 339-347 ◽  
Author(s):  
Alfredo De Bustos ◽  
Yolanda Loarce ◽  
Nicolás Jouve
Keyword(s):  
Concerted Evolution ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Diploid Species ◽  
Species Relationships ◽  
Nuclear Rdna ◽  
Hordeum Murinum ◽  
Internal Transcribed Spacer Sequences ◽  
Antifungal Chitinase

The sequences of the chitinase gene (Chi-26) and the internal transcribed spacer of 18S – 5.8S – 26S rDNA (ITS1) were determined to analyze the phylogenetic relationships among species representing the four basic genomes of the genus Hordeum. Grouping analysis based on data for Chi-26 gene sequences placed Hordeum secalinum (H genome) near the Hordeum murinum complex (Xu genome), and Hordeum bulbosum distant from the other species that carried the I genome. ITS sequence data showed the expected grouping based on the genome classification of the species studied. Different sequences of ITS were detected even in the genomes of the diploid species. The results are interpreted in terms of defective or unfinished concerted evolution processes in each taxon.Key words: ITS, Hordeum, phylogeny, chitinase, concerted evolution.

scholarly journals A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Kirk Overmyer
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Host Plants ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Rapid Identification ◽  
Nuclear Ribosomal Dna ◽  
Species Relationships ◽  
Internal Transcribed Spacer Sequences

AbstractProtomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

scholarly journals Re-Evaluation of the Order Sordariales: Delimitation of Lasiosphaeriaceae s. str., and Introduction of the New Families Diplogelasinosporaceae, Naviculisporaceae, and Schizotheciaceae

2020 ◽  
Vol 8 (9) ◽  
pp. 1430
Author(s):  
Yasmina Marin-Felix ◽  
Andrew N. Miller ◽  
José F. Cano-Lira ◽  
Josep Guarro ◽  
D. García ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Large Subunit ◽  
Apical Cell ◽  
New Genera ◽  
Nuclear Rdna ◽  
Internal Transcribed Spacer Region ◽  
Natural Classification ◽  
Reference Strains

The order Sordariales includes the polyphyletic family Lasiosphaeriaceae, which comprises approximately 30 genera characterized by its paraphysate ascomata, asci with apical apparati, and mostly two-celled ascospores, which have a dark apical cell and a hyaline lower cell, frequently ornamented with mucilaginous appendages. To produce a more natural classification of this family, we carried out a phylogenetic analysis based on sequences of the internal transcribed spacer region (ITS), the nuclear rDNA large subunit (LSU), and fragments of ribosomal polymerase II subunit 2 (rpb2) and β-tubulin (tub2) genes of several isolates from soil and of reference strains of the Sordariales. As a result, Lasiosphaeriaceae s. str. has been circumscribed for the clade including the type species of the genus Lasiosphaeria and, consequently, its description emended. In addition, the new families Diplogelasinosporaceae, Naviculisporaceae, and Schizotheciaceae are introduced to accommodate those taxa located far from the Lasiosphaeriaceae s. str. Moreover, we propose the erection of the new genera Areotheca, Lundqvistomyces, Naviculispora, Pseudoechria, Pseudoschizothecium, and Rhypophila based on morphological and sequence data. New combinations for several species of the genera Cladorrhinum, Jugulospora, Podospora, Schizothecium, and Triangularia are proposed, their descriptions are emended, and dichotomous keys are provided to discriminate among their species.

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Hydrobiologia ◽  
2006 ◽  
Vol 575 (1) ◽  
pp. 315-327 ◽  
Author(s):  
Zimin Hu ◽  
Xiaoqi Zeng ◽  
Alan T. Critchley ◽  
Steve L. Morrell ◽  
Delin Duan
Keyword(s):  
Internal Transcribed Spacer ◽  
Chondrus Crispus ◽  
Nuclear Rdna ◽  
Internal Transcribed Spacer Sequences ◽  
Northern Atlantic

Phylogenetic relationships of species in Pseudoroegneria (Poaceae: Triticeae) and related genera inferred from nuclear rDNA ITS (internal transcribed spacer) sequences

Biologia ◽  
2008 ◽  
Vol 63 (4) ◽  
Author(s):  
Haiqing Yu ◽  
Xing Fan ◽  
Chun Zhang ◽  
Chunbang Ding ◽  
Xiaoli Wang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
New Genus ◽  
The Other ◽  
Its Sequences ◽  
Agropyron Cristatum ◽  
Tetraploid Species ◽  
Nuclear Rdna ◽  
Rdna Its ◽  
Internal Transcribed Spacer Sequences

AbstractTo evaluate the phylogenetic relationships of species in Pseudoroegneria and related genera, the nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for eighteen Pseudoroegneria (St), two Elytrigia (E e St), two Douglasdeweya (StP), three Lophopyrum (E e and E b), three Agropyron (P), two Hordeum (H), two Australopyrum (W) and two Psathyrostachys (Ns) accessions. The main results were: (i) Pseudoroegneria gracillima, P. stipifolia, P. cognata and P. strigosa (2x) were in one clade, while P. libanotica, P. tauri and P. spicata (2x) were in the other clade, indicating there are the differentiations of St genome among diploid Pseudoroegneria species; (ii) P. geniculata ssp. scythica, P. geniculata ssp. pruinifera, Elytriga caespitosa and Et. caespitosa ssp. nodosa formed the E e St clade with 6-bp indel in ITS1 regions; and (iii) Douglasdeweya wangii, D. deweyi, Agropyron cristatum and A. puberulum comprised the P clade. It is unreasonable to treat P. geniculata ssp. scythica and P. geniculata ssp. pruinifera as the subspecies of P. geniculata, and they should be transferred to a new genus Trichopyrum, which consists of species with E e St genomes. It is also suggested that one of the diploid donor of D. wangii and D. deweyi is derived from Agropyron species, and it is reasonable to treat tetraploid species with StP genomes into Douglasdeweya.

Phylogenetic relationships in the Mediterranean Helichrysum (Asteraceae, Gnaphalieae) based on nuclear rDNA ITS sequence data

2004 ◽  
Vol 17 (3) ◽  
pp. 241 ◽  
Author(s):  
M. Galbany-Casals ◽  
N. Garcia-Jacas ◽  
A. Susanna ◽  
L. Sáez ◽  
C. Benedí
Keyword(s):  
Sequence Data ◽  
Cladistic Analysis ◽  
Mediterranean Area ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna ◽  
Generic Delimitation ◽  
Rdna Its ◽  
The Mediterranean ◽  
Sectional Classification

The internal transcribed spacers ITS1 and ITS2 of the nuclear rDNA were sequenced for 41 Helichrysum species (Gnaphalieae), focusing on the Mediterranean group of species, together with eight representatives of other genera of the Gnaphalieae, in order to check the hypothesised monophyly of the Mediterranean Helichrysum group and the correspondence of the sequence data with its traditional sectional classification. The cladistic analysis of sequence data supports monophyly of the Mediterranean Helichrysum excluding H. frigidum and H. montelinasanum. The traditional classification of the Mediterranean species into two sections, Helichrysum and Virginea, is not supported, whereas a group constituted by species from the west Mediterranean area is shown as a moderately supported monophyletic clade in the strict consensus tree. Other results also show and confirm the complexity, still not satisfactorily resolved, of the Helichrysum generic delimitation: Pseudognaphalium luteoalbum appears merged in Helichrysum whereas Helichrysum dasyanthum appears more related to Anaxeton laeve than to any Helichrysum species.

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