Evidence map›Paper›PMID 40702430›Full record

ArticleBMC genomics2025

Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.

Yi Zhou, Zhilu Sheng, Dongbin Li, Wencui Li, Yujia Peng, Zhaopeng Song, Zhanjun Quan, Yongbo Liu

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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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.

2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

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5 · Who and what money

Authors and funding

8 authors.

Yi ZhouState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
Zhilu ShengState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
Dongbin LiNingbo Forest Farm of Zhejiang, Ningbo, 315440, China.
Wencui LiState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
Yujia PengState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
Zhaopeng SongState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
Zhanjun QuanState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. quanzj@craes.org.cn.ORCID http://orcid.org/0000-0003-1618-8813
Yongbo LiuState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. liuyb@craes.org.cn.

Funding

Ministry of Ecology and Environment, The People's Republic of China 2019HJ2096001006
6 · The paper itself

Abstract

backgroundPolyploidization is one of the main mechanisms in speciation, yet its effects on the frequency and distribution of synonymous codons remain unclear, which may lead to distinct patterns of codon usage bias (CUB) in polyploid species. To detect whether the patterns of CUB change in Actinidia polyploidization events, we analyzed seven Actinidia species (two polyploid and five diploid species) and five phylogenetically related non-Actinidia species (one polyploid and four diploid species).

resultsThe GC and GC3 contents in the 12 plant genomes were below 50%, indicating a preference for A/T-rich nucleotides and A/T-ending codons in these species. The effective number of codons (ENC) and GC3s showed a left-skewed distribution pattern, suggesting that natural selection is the main factor in determining codon usage variation. The species tree inferred from relative synonymous codon usage (RSCU) of orthologs was associated with their phylogenetic relationship. No significant difference in CUB was detected among the subgenomes of A. deliciosa. Diploid A. chinensis and polyploid A. deliciosa shared some optimal codons, such as proline (CCG, CCA), glycine (GGC), and leucine (CTG). Diploid A. chinensis uniquely preferred the asparagine codons AAT and AAC, while polyploid A. deliciosa favored the optimal codons GGT (glycine), AAG (lysine), and GAT/GAC (aspartic acid). Significant correlations (S-values) of ENC and tRNA adaptation index (tAI) indicate tRNA selection effects on CUB, and the Actinidia species exhibited higher S-values (0.33-0.41) than the other non-Actinidia species (0.22-0.34).

conclusionsOur findings highlight that CUB in Actinidia was not affected by polyploidization events but by natural selection, and the dominant force of shaping CUB is tRNA availability.

Indexed as

ActinidiaCodonCodon UsagePolyploidyRNA, TransferSelection, GeneticBase CompositionEvolution, MolecularGenome, PlantPhylogenyCodonRNA, TransferActinidia deliciosaCodon biasNatural selectionPolyploidizationtRNA adaptation index

Identifiers

PMID40702430
PMCPMC12285074

What Socratic holds

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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 Socratic graph.