4.6 Article

Host-specific adaptation drove the coevolution of leek yellow stripe virus and Allium plants

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N

Adyatma Irawan Santosa et al.

Summary: Phylogenetic and evolutionary analyses of leek yellow stripe virus (LYSV) identified three major groups (S, L, and N) based on genetic variation and host species. The dN/dS values confirmed purifying selection for the P1 and CP genes, and gene flow was found between the groups. These findings support the previous classification of LYSV into three major evolutionary lineages.

VIRUS GENES (2023)

Article Biotechnology & Applied Microbiology

ICTV Virus Taxonomy Profile: Potyviridae 2022

Alice K. Inoue-Nagata et al.

Summary: The Potyviridae family includes filamentous plant viruses with specific genomic features and varying host ranges. Some members of this family can cause significant disease epidemics in cultivated plants.

JOURNAL OF GENERAL VIROLOGY (2022)

Article Multidisciplinary Sciences

Coat protein of partitiviruses isolated from mycorrhizal fungi functions as an RNA silencing suppressor in plants and fungi

Hanako Shimura et al.

Summary: Orchid seeds rely on orchid mycorrhizal fungi for germination, forming a close relationship during evolution. New partitiviruses were isolated from OM fungi, with different isolates showing varying RNA silencing suppressor activity in plants and fungi.

SCIENTIFIC REPORTS (2022)

Article Agriculture, Multidisciplinary

Leek Yellow Stripe Virus Can Adjust for Host Adaptation by Trimming the N-Terminal Domain to Allow the P1 Protein to Function as an RNA Silencing Suppressor

Jun Sasaki et al.

Summary: The length of the P1 protein of leek yellow stripe virus (LYSV) isolates in Japan varies, with the S-type P1 being shorter than the N-type P1. Both N-type and S-type P1 sequences can be found in mixed infections in garlic fields in Hokkaido. LYSV-S is detected more frequently in Allium spp. plants other than garlic in Honshu, suggesting a wider host range compared to LYSV-N. The P1 protein of LYSV has RNA silencing suppressor (RSS) activity, with the S-type P1 showing stronger RSS activity than the N-type P1.

PLANT PATHOLOGY JOURNAL (2022)

Article Virology

The recombinogenic history of turnip mosaic potyvirus reveals its introduction to Japan in the 19th century

Shusuke Kawakubo et al.

Summary: The study found a large number of recombination events in the genome of Turnip Mosaic Virus (TuMV) in Japan, and the virus spread to different parts of Japan before the 20th century. This study also emphasizes the importance of recombination events in the genome and provides an example of virus epidemiology surveying.

VIRUS EVOLUTION (2022)

Editorial Material Biochemistry & Molecular Biology

All about Allium

Michael Gross

Summary: Garlic and onions, cultivated and widely used since prehistoric times, belong to the genus Allium, which also includes hundreds of other species, some of which are popular as ornamental plants. These plants continue to present challenges and surprises to science.

CURRENT BIOLOGY (2021)

Article Virology

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets

Darren P. Martin et al.

Summary: The RDP project has developed an automated recombination analysis tool, RDP5, which is faster and more efficient than its predecessor, RDP4. Users can now analyze larger and more complex datasets with minimal manual intervention, allowing for greater flexibility and output options.

VIRUS EVOLUTION (2021)

Article Multidisciplinary Sciences

Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road

Shusuke Kawakubo et al.

Summary: The study investigates the evolutionary and phylogeographic history of plant pathogen, which provides insights into the spread of turnip mosaic potyvirus (TuMV) in Eurasia from the 17th century CE. The migration pathways of TuMV have retraced major historical trade arteries in Eurasia, with the regional variation characterized by different type patterns of recombinants.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Review Microbiology

Global Organization and Proposed Megataxonomy of the Virus World

Eugene V. Koonin et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2020)

Article Virology

Host Range Evolution of Potyviruses: A Global Phylogenetic Analysis

Benoit Moury et al.

VIRUSES-BASEL (2020)

Review Virology

The Potyviruses: An Evolutionary Synthesis Is Emerging

Adrian J. Gibbs et al.

VIRUSES-BASEL (2020)

Article Virology

Evolution of plant-virus interactions: host range and virus emergence

Michael J. McLeish et al.

CURRENT OPINION IN VIROLOGY (2019)

Article Biochemical Research Methods

Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration

Jing Yang et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Review Microbiology

Virus Latency and the Impact on Plants

Hideki Takahashi et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

In silico characterization and phylogenetic analysis of a mannose-specific lectin in Allium species

H. J. Jimenez et al.

GENETICS AND MOLECULAR RESEARCH (2019)

Article Biochemistry & Molecular Biology

TIPDATINGBEAST: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Adrien Rieux et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biotechnology & Applied Microbiology

Determinants of host species range in plant viruses

Benoit Moury et al.

JOURNAL OF GENERAL VIROLOGY (2017)

Article Biochemistry & Molecular Biology

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

Sebastian Duchene et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

Causes, consequences and solutions of phylogenetic incongruence

Anup Som

BRIEFINGS IN BIOINFORMATICS (2015)

Article Virology

Host ecology determines the dispersal patterns of a plant virus

Nidia Sequeira Trovao et al.

VIRUS EVOLUTION (2015)

Article Ecology

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

Daniel L. Rabosky et al.

METHODS IN ECOLOGY AND EVOLUTION (2014)

Article Agronomy

Diversity in Allium ampeloprasum: from small and wild to large and cultivated

Chedia Guenaoui et al.

GENETIC RESOURCES AND CROP EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

Ceiridwen J. Edwards et al.

CURRENT BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Review Plant Sciences

Potyviruses and the Digital Revolution

Adrian Gibbs et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 48 (2010)

Article Biochemistry & Molecular Biology

Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae)

Pablo Hirschegger et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2010)

Article Biochemical Research Methods

adegenet:: a R package for the multivariate analysis of genetic markers

Thibaut Jombart

BIOINFORMATICS (2008)

Article Multidisciplinary Sciences

The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture

Adrian J. Gibbs et al.

PLOS ONE (2008)

Article Biotechnology & Applied Microbiology

Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae

Adrian Valli et al.

JOURNAL OF GENERAL VIROLOGY (2007)

Article Biotechnology & Applied Microbiology

Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination

Kazusato Ohshima et al.

JOURNAL OF GENERAL VIROLOGY (2007)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biotechnology & Applied Microbiology

Molecular evolution of Turnip mosaic virus:: evidence of host adaptation, genetic recombination and geographical spread

K Ohshima et al.

JOURNAL OF GENERAL VIROLOGY (2002)