Genetics polymorphism of poplars from Moscow region based on high-throughput sequencing of ITS

Poplars are widely used in landscaping of Moscow due to the ability to effectively purify the air from harmful impurities and to release a large amount of oxygen. The genusPopulusis characterized by a high level of intraspecies polymorphism, as well as the presence of natural interspecies hybrids. The aim of our work was to evaluate the genetic diversity of poplars, which are growing on the territory of Moscow city by high-throughput sequencing of internal transcribed spacers of 45S rRNA genes (ITS sequences). Sequencing of ITS of 40 poplar plants was performed on Illumina platform (MiSeq) and about 3 000 reads were obtained for each sample in average. Bioinformatics analysis was performed using CLC Genomics Workbench tool. The involved set of poplars had a high level of genetic diversity – the number of single nucleotide polymorphisms (SNPs) detected in each genotype relative to the reference ITS1 and ITS2 sequences ofP. trichocarpavarying from 4 to 44. We showed that even trees which had been planted on the same territory and, probably, at the same time had significant genetic differences. It can be speculated that highly polymorphic plant material was used for planting poplars in Moscow. For some sites with SNPs, several variants of nucleotides were found in the same individual and the ratio of SNPs was different. We assume that close to 50/50 ratio is observed in interspecific hybrids due to genetic differences in the ITS sequences between maternal and paternal genotypes. For SNPs with a predominance of one of the variants, the presence of paralogues among numerous genomic copies of ITS sequences is more likely. The results of our work can provide a framework for molecular genetic markers application with the purpose ofPopulusspecies and interspecific hybrids identification, determination the origin of a number of natural hybrids, and monitoring the diversity of genusPopulusin the Moscow city.

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High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

Viruses ◽

10.3390/v10070385 ◽

2018 ◽

Vol 10 (7) ◽

pp. 385 ◽

Cited By ~ 4

Author(s):

Asimina Katsiani ◽

Varvara Maliogka ◽

Nikolaos Katis ◽

Laurence Svanella-Dumas ◽

Antonio Olmos ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

High Throughput Sequencing ◽

Sour Cherry ◽

Prunus Species ◽

Cherry Tree ◽

High Genetic Diversity ◽

Viral Genomes ◽

Virus Diversity ◽

First Time

Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.

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PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

Database ◽

10.1093/database/baz155 ◽

2020 ◽

Vol 2020 ◽

Cited By ~ 6

Author(s):

Elisa Banchi ◽

Claudio G Ametrano ◽

Samuele Greco ◽

David Stanković ◽

Lucia Muggia ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Its Region ◽

Computational Effort ◽

Its Sequences ◽

Reference Dataset ◽

Bioinformatic Pipeline ◽

Taxonomic Level ◽

Dna Metabarcoding ◽

Reference Databases

Abstract DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.

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Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph121012002 ◽

2015 ◽

Vol 12 (10) ◽

pp. 12002-12015 ◽

Cited By ~ 48

Author(s):

Mu Peng ◽

Xiaoxue Zi ◽

Qiuyu Wang

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

High Throughput ◽

Contaminated Soils ◽

High Throughput Sequencing ◽

Community Diversity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Community Diversity

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Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

Applied and Environmental Microbiology ◽

10.1128/aem.71.9.5544-5550.2005 ◽

2005 ◽

Vol 71 (9) ◽

pp. 5544-5550 ◽

Cited By ~ 607

Author(s):

Heath E. O'Brien ◽

Jeri Lynn Parrent ◽

Jason A. Jackson ◽

Jean-Marc Moncalvo ◽

Rytas Vilgalys

Keyword(s):

Large Scale ◽

High Throughput Sequencing ◽

Small Subunit ◽

Its Sequences ◽

High Rate ◽

Rrna Genes ◽

Soil Horizon ◽

Eukaryotic Microorganisms ◽

Sequence Types ◽

Fungal Its

ABSTRACT Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.

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Characterization of genetic diversity on tropical Trichoderma germplasm by sequencing of rRNA internal transcribed spacers

BMC Research Notes ◽

10.1186/s13104-019-4694-1 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Yara Barros Feitosa ◽

Valter Cruz-Magalhães ◽

Ronaldo Costa Argolo-Filho ◽

Jorge Teodoro de Souza ◽

Leandro Lopes Loguercio

Keyword(s):

Genetic Diversity ◽

Molecular Level ◽

Its Region ◽

Internal Transcribed Spacers ◽

Plant Diseases ◽

Rrna Genes ◽

Physiological Data ◽

Biotic And Abiotic Stresses ◽

Beneficial Effects

Abstract Objective Trichoderma species are found in soil and in association with plants. They can act directly or indirectly in the biological control of plant diseases and in the promotion of plant growth, being among the most used fungi in the formulation of bioproducts applied to agricultural systems. The main objective of this study was to characterize at a first-tier level a collection of 67 Trichoderma isolates from various tropical sources, based solely on sequencing of the internal transcribed spacer (ITS) region of the rRNA genes. Our goal was to provide a preliminary idea of the baseline diversity in this collection, to combine this information later with an array of other isolate-specific physiological data. This study provides a required knowledge at molecular level for assessment of this germplasm potential as a source of biotechnological products for beneficial effects in plants. Results Sequencing of the ITS region showed that the 67 Trichoderma isolates belonged in 11 species: T. asperellum, T. atroviride, T. brevicompactum, T. harzianum, T. koningiopsis, T. longibrachiatum, T. pleuroticola, T. reesei, T. spirale, T. stromaticum and T. virens. A total of 40.3% of the isolates were very closely related to each other and similar to T. harzianum. The baseline genetic diversity found indicates that the collection has different genotypes, which can be exploited further as a source of bioproducts, aiming at providing beneficial effects to plants of interest to cope with biotic and abiotic stresses.

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