Evidence map›Paper›PMID 40004530›Full record

ArticleGenes2025

Comparative Chloroplast Genomics and Codon Usage Bias Analysis in

Yang Yang, Xueyang Liu, Lixia He, Zhenhua Li, Boxuan Yuan, Fengyan Fang, Mei Wang, Aifang Li, Cheng Liu, Minmin He and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Complete Chloroplast Genome Analysis ofPlants (Basel, Switzerland) · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Yang YangPlant Stress Resistance Integrated Biology Laboratory, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
Xueyang LiuPhotosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Lixia HePlant Stress Resistance Integrated Biology Laboratory, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
Zhenhua LiPhotosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Boxuan YuanKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Fengyan FangKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Mei WangKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Aifang LiKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Cheng LiuPhotosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Minmin HeKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.ORCID 0009-0006-6023-9285
Shugang HuiKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Wenda WangPhotosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Xuchu WangPlant Stress Resistance Integrated Biology Laboratory, College of Life Sciences, Hainan Normal University, Haikou 571158, China.

Funding

the CAS Project for Young Scientists in Basic Research YSBR-093the Innovation Center for Academicians of Hainan Province and the Specific Research Fund of the Innovation Platform for Academicians of Hainan Province No. YSPTZX202309the National Key Research and Development Program of China No. 2021YFA1300401 and 2021YFA1300403the Special Fund of Guizhou University LJ2023-03
6 · The paper itself

Abstract

objectivesThis study investigates the cpDNA sequences from six

methodscpDNA sequences from six

resultsThe cpDNAs from the six species exhibited genome sizes ranging from 161,093 bp to 161,254 bp, with GC content between 35.72% and 35.75%. Each genome contained 91 to 92 protein-coding genes, with the infA gene consistently present. No significant gene rearrangements were detected, and SSR analysis revealed mono-repeats primarily composed of A/T bases. Codon usage analysis indicated that leucine is predominantly encoded by the UUA codon, and 31 optimal codons were identified, mainly ending in A or U. Phylogenetic analysis clarified the genetic relationships among the species.

conclusionsThe study provides detailed insights into the cpDNA characteristics of

Indexed as

ChloroplastsCodon UsageGenome, ChloroplastBase CompositionCodonDNA, ChloroplastGenomicsMicrosatellite RepeatsPhylogenyCodonDNA, Chloroplastchloroplast genomecodonHeveaRSCU

Identifiers

PMID40004530
PMCPMC11855534

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Registered trials

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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 OpenQuestion graph.