4.6 Article

Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Loss and Natural Variations of Blast Fungal Avirulence Genes Breakdown Rice Resistance Genes in the Sichuan Basin of China

Zi-Jin Hu et al.

Summary: This study analyzed the nucleotide sequence polymorphisms of eight known AVR genes in 383 isolates from different prefectures in the Sichuan Basin. The results showed the presence of five AVR genes in all isolates, while three other AVR genes were absent in at least seven prefectures.

FRONTIERS IN PLANT SCIENCE (2022)

Editorial Material Biochemistry & Molecular Biology

Super graph-based pan-genome: Bringing rice functional genomic study into a new dawn

Yucheng Liu et al.

MOLECULAR PLANT (2022)

Article Microbiology

Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus

Maria Augusta C. Horta et al.

Summary: This study investigated the genomic variation in 206 Aspergillus fumigatus isolates and found that there were differences in gene distribution among isolates, but these differences were not related to the clinical or environmental origin of the isolates.
Article Cell Biology

A super pan-genomic landscape of rice

Lianguang Shang et al.

Summary: By studying the pan-genomes of large natural populations, we can uncover the genetic diversity and complexity of rice. We have created a super pan-genome of rice using long-read assembly and identified extensive structural variations and gene presence/absence variations. Additionally, we have discovered genetic variants associated with various traits in rice and identified a common set of genes that have played a role in adaptation and domestication in Asian and African rice.

CELL RESEARCH (2022)

Article Genetics & Heredity

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus

Thorsten Langner et al.

Summary: Supernumerary mini-chromosomes in the blast fungus M. oryzae are highly diverse and enriched in repetitive genetic elements, with lower gene density compared to core-chromosomes. These mini-chromosomes may emerge from structural rearrangements and segmental duplication of core-chromosomes, contributing to the adaptive evolution of the fungus. They contain virulence-related genes and are involved in large-scale genomic rearrangements, indicating their role in facilitating genome dynamics and potentially adaptive evolution.

PLOS GENETICS (2021)

Article Microbiology

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

Amelia E. Barber et al.

Summary: The study identified the pan-genome of Aspergillus fumigatus using 300 globally sampled genomes, with findings showing the presence of core genes in all isolates alongside variability in 16-22% of the genome. Clinical isolates were found to be enriched in a genetic cluster with more accessory genes related to transporters, iron-binding activity, and metabolism. Genome-wide association studies revealed genetic variation associated with human infection and drug resistance, providing insight into potential therapeutic targets.

NATURE MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Peng Qin et al.

Summary: The study assembled high-quality genomes of genetically diverse rice accessions, discovering a large number of structural variations and gene copy number variations. By using a graph-based genome, the research explored the impact of these variations on rice domestication and environmental adaptation.
Article Evolutionary Biology

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae

David E. Torres et al.

Summary: Transposable elements (TEs) are important sources of genetic and regulatory variation in host genomes, playing significant roles in evolution. In the fungal plant pathogen V. dahliae, polymorphic TEs are associated with genomic variation, expression of pathogenicity-related genes, and potentially impact the evolution of adaptive genomic regions.

GENOME BIOLOGY AND EVOLUTION (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Genetics & Heredity

Pan-genomics in the human genome era

Rachel M. Sherman et al.

NATURE REVIEWS GENETICS (2020)

Article Multidisciplinary Sciences

The pan-genome effector-triggered immunity landscape of a host-pathogen interaction

Bradley Laflamme et al.

SCIENCE (2020)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Review Microbiology

The birth and death of effectors in rapidly evolving filamentous pathogen genomes

Simone Fouche et al.

CURRENT OPINION IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wensheng Wang et al.

NATURE (2018)

Review Biotechnology & Applied Microbiology

Ten things you should know about transposable elements

Guillaume Bourque et al.

GENOME BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

Luigi Faino et al.

GENOME RESEARCH (2016)

Article Multidisciplinary Sciences

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

Zhenhui Zhong et al.

SCIENTIFIC REPORTS (2016)

Article Cell Biology

The two-speed genomes of filamentous pathogens: waltz with plants

Suomeng Dong et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2015)

Review Biochemistry & Molecular Biology

The population biology of fungal invasions

P. Gladieux et al.

MOLECULAR ECOLOGY (2015)

Article Genetics & Heredity

Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae

Ju Huang et al.

BMC GENETICS (2014)

Article Biochemistry & Molecular Biology

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

Bastian Pfeifer et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Multidisciplinary Sciences

Lineage Selection and the Maintenance of Sex

Damien M. de Vienne et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Li-Jun Ma et al.

NATURE (2010)

Article Multidisciplinary Sciences

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:: Implications for the microbial pan-genome

H Tettelin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)