4.8 Article

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum

Related references

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

Deeply conserved synteny and the evolution of metazoan chromosomes

Oleg Simakov et al.

Summary: This study reveals chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges, and reconstructs ancestral chromosomes across major animal groups through comparative analysis. This provides insights into the processes of chromosome evolution and establishes a unified framework for metazoan chromosome evolution.

SCIENCE ADVANCES (2022)

Review Genetics & Heredity

The evolution of the GALactose utilization pathway in budding yeasts

Marie-Claire Harrison et al.

Summary: This review highlights recent exciting research on three different aspects of the evolution of the GAL pathway: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.

TRENDS IN GENETICS (2022)

Article Biochemistry & Molecular Biology

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

Abigail Leavitt LaBella et al.

Summary: Reverse ecology involves inferring ecological information from patterns of genomic variation, with a focus on codon optimality. The study found a positive correlation between optimal codon usage in the galactose metabolism pathway and quantitative growth on galactose, as well as associations with human-associated and dairy-associated ecological niches in yeasts. This suggests that codon optimization can provide insights into the metabolic ecology of microbial eukaryotes, particularly for studying fungal dark matter species.

PLOS BIOLOGY (2021)

Article Multidisciplinary Sciences

Whole-genome microsynteny-based phylogeny of angiosperms

Tao Zhao et al.

Summary: Plant genomes vary greatly in size, organization, and architecture, with structural differences providing valuable information for phylogenetic inference. A new method combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference has been developed to reconstruct phylogenies based on microsynteny information, showing accuracy, consistency, and wide applicability. This synteny-based approach complements traditional methods and offers insights into long-standing controversial phylogenetic relationships.

NATURE COMMUNICATIONS (2021)

Article Genetics & Heredity

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss

Max A. B. Haase et al.

Summary: Dollo's law suggests that evolutionary losses are irreversible, but a study on yeast shows that traits lost millions of years ago can be reacquired through horizontal gene transfer, demonstrating that reversals to ancestral states are possible.

GENETICS (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Guenola Drillon et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Ecology

Deeply conserved synteny resolves early events in vertebrate evolution

Oleg Simakov et al.

NATURE ECOLOGY & EVOLUTION (2020)

Review Biotechnology & Applied Microbiology

Hybridization and the origin of new yeast lineages

Toni Gabaldon

FEMS YEAST RESEARCH (2020)

Article Multidisciplinary Sciences

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Xing-Xing Shen et al.

SCIENCE ADVANCES (2020)

Article Multidisciplinary Sciences

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

Tao Zhao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

Jacob L. Steenwyk et al.

PLOS BIOLOGY (2019)

Article Biotechnology & Applied Microbiology

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

Xin Qiao et al.

GENOME BIOLOGY (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

Robert M. Waterhouse et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Multidisciplinary Sciences

GOATOOLS: A Python library for Gene Ontology analyses

D. V. Klopfenstein et al.

SCIENTIFIC REPORTS (2018)

Review Microbiology

The birth, evolution and death of metabolic gene clusters in fungi

Antonis Rokas et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Article Biochemistry & Molecular Biology

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Xing-Xing Shen et al.

Article Genetics & Heredity

Correction: The Evolution of Fungal Metabolic Pathways

Jennifer H. Wisecaver et al.

PLoS Genetics (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Review Biotechnology & Applied Microbiology

Genome structure and dynamics of the yeast pathogen Candida glabrata

Khadija M. Ahmad et al.

FEMS YEAST RESEARCH (2014)

Article Multidisciplinary Sciences

Insights into bilaterian evolution from three spiralian genomes

Oleg Simakov et al.

NATURE (2013)

Article Multidisciplinary Sciences

Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds

Kriston L. McGary et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Ecology

phytools: an R package for phylogenetic comparative biology (and other things)

Liam J. Revell

METHODS IN ECOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

Positional orthology: putting genomic evolutionary relationships into context

Colin N. Dewey

BRIEFINGS IN BIOINFORMATICS (2011)

Article Biology

Comparative study on synteny between yeasts and vertebrates

Guenola Drillon et al.

COMPTES RENDUS BIOLOGIES (2011)

Article Biotechnology & Applied Microbiology

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

James K. Hane et al.

GENOME BIOLOGY (2011)

Article Multidisciplinary Sciences

Remarkably ancient balanced polymorphisms in a multi-locus gene network

Chris Todd Hittinger et al.

NATURE (2010)

Article Multidisciplinary Sciences

Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

Jason C. Slot et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

Evolution of genome architecture

Eugene V. Koonin

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2009)

Review Genetics & Heredity

Phylogenomics and the reconstruction of the tree of life

F Delsuc et al.

NATURE REVIEWS GENETICS (2005)

Article Multidisciplinary Sciences

Genome evolution in yeasts

B Dujon et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Multidisciplinary Sciences

The hidden duplication past of Arabidopsis thaliana

C Simillion et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

The evolutionary fate and consequences of duplicate genes

M Lynch et al.

SCIENCE (2000)

Review Plant Sciences

Synteny: recent advances and future prospects

R Schmidt

CURRENT OPINION IN PLANT BIOLOGY (2000)