4.7 Article

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Synonymous mutations in representative yeast genes are mostly strongly non-neutral

Xukang Shen et al.

Summary: Synonymous mutations in protein-coding genes are not neutral and often result in reduced fitness and disturbed mRNA expression levels. Non-synonymous mutations have greater fitness variations across environments, which may explain the lower substitution rates compared to synonymous mutations.

NATURE (2022)

Article Biochemistry & Molecular Biology

Extensive variation in nucleotide substitution rate and gene/intron loss in mitochondrial genomes of Pelargonium

KyoungSu Choi et al.

Summary: The organelle genomes of Geraniaceae plants exhibit highly unusual features compared to other angiosperms, including rearranged plastomes, gene and intron loss, accelerated nucleotide substitution rates, and biparental inheritance of the plastome. A study examining 27 species of Geraniales, including 13 species of Pelargonium, found extensive gene and intron losses across the family. Pelargonium had the most gene depauperate lineage, with gene losses occurring multiple times and intron losses reflecting taxonomic relationships. Pelargonium showed elevated nucleotide substitution rates in both mitochondrial and plastid genes, different from most angiosperms, with potential different causes for substitutions in each organelle.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Genetics & Heredity

Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

Wenjing Xu et al.

Summary: Asymmetric somatic hybridization affects synonymous codon usage bias (SCUB) and promotes a bias towards A- and T-ending synonymous codons, with a stronger effect in indel-flanking sequences. This shift is attributed to whole genomic shock, and DNA methylation may play a role in SCUB shift during asymmetric somatic hybridization. Exogenous chromatin fragments introduced through this strategy do not have a local chromosomal effect on SCUB frequencies.

FRONTIERS IN GENETICS (2021)

Article Biochemistry & Molecular Biology

Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

Yixuan Kou et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Review Cell Biology

Codon optimality, bias and usage in translation and mRNA decay

Gavin Hanson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Review Genetics & Heredity

The rice genome revolution: from an ancient grain to Green Super Rice

Rod A. Wing et al.

NATURE REVIEWS GENETICS (2018)

Article Genetics & Heredity

Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids

Jasdeep S. Mutti et al.

G3-GENES GENOMES GENETICS (2017)

Review Plant Sciences

Gene body DNA methylation in plants

Adam J. Bewick et al.

CURRENT OPINION IN PLANT BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Codon Optimality Is a Major Determinant of mRNA Stability

Vladimir Presnyak et al.

Article Biochemistry & Molecular Biology

The Curious Chemical Biology of Cytosine: Deamination, Methylation,and Oxidation as Modulators of Genomic Potential

Christopher S. Nabel et al.

ACS CHEMICAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Higher Intron Loss Rate in Arabidopsis thaliana Than A-lyrata Is Consistent with Stronger Selection for a Smaller Genome

Jeffrey A. Fawcett et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Multidisciplinary Sciences

A map of rice genome variation reveals the origin of cultivated rice

Xuehui Huang et al.

NATURE (2012)

Review Genetics & Heredity

Synonymous but not the same: the causes and consequences of codon bias

Joshua B. Plotkin et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemistry & Molecular Biology

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

Tamir Tuller et al.

Review Genetics & Heredity

Principles and challenges of genome-wide DNA methylation analysis

Peter W. Laird

NATURE REVIEWS GENETICS (2010)

Article Multidisciplinary Sciences

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

Stephan Ossowski et al.

SCIENCE (2010)

Article Anthropology

Consilience of genetics and archaeobotany in the entangled history of rice

Dorian Q. Fuller et al.

ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES (2010)

Article Biochemistry & Molecular Biology

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

Jian-Qun Chen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

Gong Zhang et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Review Genetics & Heredity

Selection on Codon Bias

Ruth Hershberg et al.

ANNUAL REVIEW OF GENETICS (2008)

Article Biochemistry & Molecular Biology

The pattern of insertion/deletion polymorphism in Arabidopsis thaliana

Wen Zhang et al.

MOLECULAR GENETICS AND GENOMICS (2008)

Article Multidisciplinary Sciences

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

Dacheng Tian et al.

NATURE (2008)

Article Multidisciplinary Sciences

Alternative splicing:: A missing piece in the puzzle of intron gain

Rosa Tarrio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biotechnology & Applied Microbiology

Mechanisms of intron gain and loss in Cryptococcus

Thomas J. Sharpton et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Characterization of intron loss events in mammals

Jasmin Coulombe-Huntington et al.

GENOME RESEARCH (2007)

Article Biochemistry & Molecular Biology

High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes

David G. Knowles et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Multidisciplinary Sciences

Rice domestication by reducing shattering

CB Li et al.

SCIENCE (2006)

Article Cell Biology

Gene expression and molecular evolution

H Akashi

CURRENT OPINION IN GENETICS & DEVELOPMENT (2001)

Article Multidisciplinary Sciences

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

G Marais et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Review Genetics & Heredity

Isochores and the evolutionary genomics of vertebrates

G Bernardi