ArticleGenome biology and evolution2014
The bimodal distribution of genic GC content is ancestral to monocot species.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Article
- Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis.BMC plant biology · 2024Article
- The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay.Genome biology · 2024Article
- GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2.BMC plant biology · 2023Article
- Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus.G3 (Bethesda, Md.) · 2022Article
- Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms.Zoological research · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- A comprehensive map of preferentially located motifs reveals distinct proximalFrontiers in plant science · 2022Article
- Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species.Frontiers in genetics · 2021Article
- GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals.Genome biology and evolution · 2019Article
- GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution.BMC evolutionary biology · 2019Article
- The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.Nucleic acids research · 2018Article
- Codon usage vis-a-vis start and stop codon context analysis of three dicot species.Journal of genetics · 2018Article
- Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA.Genome biology and evolution · 2018Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.BMC bioinformatics · 2017Article
- The Evolutionary Basis of Translational Accuracy in Plants.G3 (Bethesda, Md.) · 2017Article
- Evolutionary forces affecting synonymous variations in plant genomes.PLoS genetics · 2017Article
- Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation.G3 (Bethesda, Md.) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In grasses such as rice or maize, the distribution of genic GC content is well known to be bimodal. It is mainly driven by GC content at third codon positions (GC3 for short). This feature is thought to be specific to grasses as closely related species like banana have a unimodal GC3 distribution. GC3 is associated with numerous genomics features and uncovering the origin of this peculiar distribution will help understanding the potential roles and consequences of GC3 variations within and between genomes. Until recently, the origin of the peculiar GC3 distribution in grasses has remained unknown. Thanks to the recent publication of several complete genomes and transcriptomes of nongrass monocots, we studied more than 1,000 groups of one-to-one orthologous genes in seven grasses and three outgroup species (banana, palm tree, and yam). Using a maximum likelihood-based method, we reconstructed GC3 at several ancestral nodes. We found that the bimodal GC3 distribution observed in extant grasses is ancestral to both grasses and most monocot species, and that other species studied here have lost this peculiar structure. We also found that GC3 in grass lineages is globally evolving very slowly and that the decreasing GC3 gradient observed from 5' to 3' along coding sequences is also conserved and ancestral to monocots. This result strongly challenges the previous views on the specificity of grass genomes and we discuss its implications for the possible causes of the evolution of GC content in monocots.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.