Molecular diversity of ericoid mycorrhizal fungi

2000 ◽  
Vol 77 (11) ◽  
pp. 1580-1594
Author(s):  
Marcia Monreal ◽  
S M Berch ◽  
Mary Berbee
Keyword(s):  
Sequence Analysis ◽  
Dna Sequences ◽  
Mycorrhizal Fungi ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Field Site ◽  
Specific Primers ◽  
Single Root ◽  
Ericoid Mycorrhizal Fungi

Using restriction fragment length polymorphism (RFLP) patterns from two ribosomal internal transcribed spacers (ITS) and DNA sequences from ITS2, we characterized ericoid mycorrhizal fungal isolates from culture collections.With a synoptic key to RFLP patterns, we divided 34 mycorrhizal or root-associated isolates into 16 groups. RFLP patterns were identical when fungal specific primers were used to amplify DNA from pure fungal cultures and in vitro mycorrhizae. Sequence analysis clustered 23 of 24 mycorrhizal isolates into two larger groups: the Oidiodendron group and the Hymenoscyphus group. The Oidiodendron group included genetically uniform, conidiating fungi. The Hymenoscyphus group encompassed more diversity and included other discomycetes (Leotiales) as well as sterile, unidentifiable mycorrhizal isolates from four RFLP groups. Results from our field site on Vancouver Island, British Columbia, Canada, suggest that several ericoid mycorrhizal fungi can coexist in a single root of Gaultheria shallon Pursh and that our molecular data base is not yet complete. From sixty 3-mm root sections, we cultured four genetically different fungi that formed mycorrhizae in resynthesis experiments and sequence analysis showed that one of these differed from all previously known ericoid mycorrhizal fungi.

Phylogenetic analysis of Gyrodactylus spp. (Platyhelminthes: Monogenea) using ribosomal DNA sequences

1999 ◽  
Vol 77 (9) ◽  
pp. 1439-1449 ◽  
Author(s):  
J Cable ◽  
P D Harris ◽  
R C Tinsley ◽  
C M Lazarus
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Species Group ◽  
Internal Transcribed Spacers ◽  
Base Pairs ◽  
Separate Species ◽  
5.8S Rdna ◽  
Complete Sequences

Species of the viviparous monogenean genus Gyrodactylus are difficult to identify morphologically and relationships within the genus are unclear. Partial or complete sequences were obtained for the internal transcribed spacers (ITS-1 and ITS-2) and 5.8S ribosomal DNA (rDNA) of 11 Gyrodactylus species (G. kobayashii, G. gurleyi, G. pungitii, G. rogatensis, G. gasterostei, G. derjavini, G. salaris, G. rarus, G. turnbulli, G. bullatarudis, and G. arcuatus) and the related Gyrdicotylus gallieni. Phylogenetic analyses (parsimony, distance, and maximum likelihood) separated species of the Gyrodactylus wageneri species-group (with a long ITS-1) from those of the Gyrodactylus eucaliae and G. arcuatus species-groups (with a short ITS-1). This subdivision into species with a long (610-630 base pairs (bp)) or short (300-500 bp) ITS-1 was also apparent with 5.8S rDNA and ITS-2 data. No support could be found for the hypothesis that G. salaris is a member of a separate species group, as this species clustered within the G. wageneri group. The morphologically homogeneous G. wageneri group was subdivided by our molecular data into five species that infect cottids, gasterosteids, and salmonids and two species that infect cyprinid fishes. Overall, the ITS-2, combined with the 5.8S rDNA (an alignment of 668 bp), appeared to be the most informative indicator of phylogenetic relationships within the genus Gyrodactylus. The potential importance of this technique for future gyrodactylid systematics is discussed.

scholarly journals Interactions of ericoid mycorrhizal fungi and root pathogens in Rhododendron: In vitro tests with plantlets in sterile liquid culture

Plant Root ◽  
2013 ◽  
Vol 7 (0) ◽  
pp. 33-48 ◽  
Author(s):  
Gisela Grunewaldt-Stöcker ◽  
Christiane von den Berg ◽  
Johanna Knopp ◽  
Henning von Alten
Keyword(s):  
Mycorrhizal Fungi ◽  
Liquid Culture ◽  
Ericoid Mycorrhizal Fungi ◽  
Root Pathogens

scholarly journals In Vitro Colonization of Micropropagated Pieris floribunda by Ericoid Mycorrhizae. II. Effects on Acclimatization and Growth

HortScience ◽  
2001 ◽  
Vol 36 (2) ◽  
pp. 357-359 ◽  
Author(s):  
Mark C. Starrett ◽  
Frank A. Blazich ◽  
Steven R. Shafer ◽  
Larry F. Grand
Keyword(s):  
Mycorrhizal Fungi ◽  
Hymenoscyphus Ericae ◽  
Ericoid Mycorrhizal Fungi ◽  
Ericoid Mycorrhizae ◽  
In Vitro Inoculation

Inoculation of microshoots of Pieris floribunda (Pursh ex Sims) Benth. and Hook. (mountain andromeda) with isolates of Hymenoscyphus ericae (Read) Korf and Kernan ericoid mycorrhizal fungi stimulated growth during 1 month in vitro. However, no benefits were apparent after 3 months in a greenhouse. Acclimatization of plantlets of P. floribunda to greenhouse conditions following in vitro inoculation improved survival (42% vs. 16% for controls). The protocol reported herein is similar to procedures utilized currently for micropropagation of various ericaceous species and has potential to improve plantlet survival during acclimatization.

scholarly journals FastSK: fast sequence analysis with gapped string kernels

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i857-i865
Author(s):  
Derrick Blakely ◽  
Eamon Collins ◽  
Ritambhara Singh ◽  
Andrew Norton ◽  
Jack Lanchantin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Sequences ◽  
English Language ◽  
Computation Time ◽  
Entity Recognition ◽  
Supplementary Information ◽  
Support Vector ◽  
Homology Detection ◽  
Scalable Algorithm ◽  
String Kernels

Abstract Motivation Gapped k-mer kernels with support vector machines (gkm-SVMs) have achieved strong predictive performance on regulatory DNA sequences on modestly sized training sets. However, existing gkm-SVM algorithms suffer from slow kernel computation time, as they depend exponentially on the sub-sequence feature length, number of mismatch positions, and the task’s alphabet size. Results In this work, we introduce a fast and scalable algorithm for calculating gapped k-mer string kernels. Our method, named FastSK, uses a simplified kernel formulation that decomposes the kernel calculation into a set of independent counting operations over the possible mismatch positions. This simplified decomposition allows us to devise a fast Monte Carlo approximation that rapidly converges. FastSK can scale to much greater feature lengths, allows us to consider more mismatches, and is performant on a variety of sequence analysis tasks. On multiple DNA transcription factor binding site prediction datasets, FastSK consistently matches or outperforms the state-of-the-art gkmSVM-2.0 algorithms in area under the ROC curve, while achieving average speedups in kernel computation of ∼100× and speedups of ∼800× for large feature lengths. We further show that FastSK outperforms character-level recurrent and convolutional neural networks while achieving low variance. We then extend FastSK to 7 English-language medical named entity recognition datasets and 10 protein remote homology detection datasets. FastSK consistently matches or outperforms these baselines. Availability and implementation Our algorithm is available as a Python package and as C++ source code at https://github.com/QData/FastSK Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Morphological and Genetic Structure of Two Equivalent Astyanax Species (Characiformes: Characidae) in the Region of Paranaíba Arc

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Renan Rodrigues Rocha ◽  
Rosana de Mesquita Alves ◽  
Rubens Pasa ◽  
Karine Frehner Kavalco
Keyword(s):  
Geometric Morphometrics ◽  
River Basin ◽  
Dna Sequences ◽  
Haplotype Network ◽  
River Basins ◽  
Molecular Data ◽  
The Body ◽  
Present Species ◽  
Body Depth ◽  
Geometric Morphometric

The Astyanax scabripinnis complex is composed of a large number of almost morphological indistinguishable species, including Astyanax paranae and Astyanax rivularis, which exist in the Paraná and São Francisco Basins, respectively, and sometimes are considered subspecies of the A. scabripinnis group or even are cited just as A. scabripinnis. The two river basins are separated by the Upper Paranaíba Arc, likely the main cause of the isolation of these species. We used geometric morphometric tools and DNA analyses of populations of both species to identify the differences between them. Geometric morphometrics separated the two species into distinct groups, whose main difference was the body depth. This is generally related to the speed of the water flow in the river basins. The maximum likelihood phylogram based on mitochondrial DNA sequences formed two main clades: one composed of the population of A. rivularis and the other, of A. paranae. In the haplotype network, the species were similarly separated into two groups from the same ancestral haplotype, with A. rivularis dispersing into two lineages in the São Francisco River Basin. The distribution of A. paranae is a consequence of a secondary dispersion event in the Paraná River Basin. It forms two lineages from a haplotype derived from the ancestor. The vicariant effect of separate basins, through the elevation of the Upper Paranaíba Arc, led to the allopatric speciation of the populations originating the present species. The results of geometric morphometrics and molecular data of the fish show the importance of this geological event in the biogeography and evolutionary history of the ichthyofauna of the region and indicate that the isolation of these species seems to be effective.

scholarly journals Biological Impact of a Large-Scale Genomic Inversion That Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of theStreptococcus pyogenesChromosome

2019 ◽  
Vol 201 (17) ◽  
Author(s):  
Dragutin J. Savic ◽  
Scott V. Nguyen ◽  
Kimberly McCullor ◽  
W. Michael McShan
Keyword(s):  
Dna Sequences ◽  
Parental Strain ◽  
Large Scale ◽  
Galleria Mellonella ◽  
Acute Infection ◽  
Relative Length ◽  
Published Data ◽  
Rich Medium ◽  
Content Type

ABSTRACTA large-scale genomic inversion encompassing 0.79 Mb of the 1.816-Mb-longStreptococcus pyogenesserotype M49 strain NZ131 chromosome spontaneously occurs in a minor subpopulation of cells, and in this report genetic selection was used to obtain a stable lineage with this chromosomal rearrangement. This inversion, which drastically displaces theorisite relative to the terminus, changes the relative length of the replication arms so that one replichore is approximately 0.41 Mb while the other is about 1.40 Mb in length. Genomic reversion to the original chromosome constellation is not observed in PCR-monitored analyses after 180 generations of growth in rich medium. Compared to the parental strain, the inversion surprisingly demonstrates a nearly identical growth pattern in the first phase of the exponential phase, but differences do occur when resources in the medium become limited. When cultured separately in rich medium during prolonged stationary phase or in an experimental acute infection animal model (Galleria mellonella), the parental strain and the invertant have equivalent survival rates. However, when they are coincubated together, bothin vitroandin vivo, the survival of the invertant declines relative to the level for the parental strain. The accompanying aspect of the study suggests that inversions taking place nearoriCalways happen to secure the linkage oforiCto DNA sequences responsible for chromosome partition. The biological relevance of large-scale inversions is also discussed.IMPORTANCEBased on our previous work, we created to our knowledge the largest asymmetric inversion, covering 43.5% of theS. pyogenesgenome. In spite of a drastic replacement of origin of replication and the unbalanced size of replichores (1.4 Mb versus 0.41 Mb), the invertant, when not challenged with its progenitor, showed impressive vitality for growthin vitroand in pathogenesis assays. The mutant supports the existing idea that slightly deleterious mutations can provide the setting for secondary adaptive changes. Furthermore, comparative analysis of the mutant with previously published data strongly indicates that even large genomic rearrangements survive provided that the integrity of theoriCand the chromosome partition cluster is preserved.

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