Patterns of synonymous codon usage bias in chloroplast genomes of seed plants

2008 ◽  
Vol 10 (4) ◽  
pp. 235-242 ◽  
Author(s):  
Meng Zhou ◽  
Wei Long ◽  
Xia Li
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Seed Plants ◽  
Chloroplast Genomes ◽  
Synonymous Codon Usage Bias

scholarly journals Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242624
Author(s):  
Geng Tian ◽  
Guoqing Li ◽  
Yanling Liu ◽  
Qinghua Liu ◽  
Yanxia Wang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Bread Wheat ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Tetraploid Cotton ◽  
Diploid Progenitor ◽  
Crop Species ◽  
Chloroplast Genomes ◽  
Synonymous Codon Usage Bias

Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants, SCUB. Its effect on organellar genes has not, however, been widely addressed. The present analysis targeted the chloroplast genomes of two leading polyploid crop species, namely cotton and bread wheat. The frequency of codons in the chloroplast genomes ending in either adenosine (NNA) or thymine (NNT) proved to be higher than those ending in either guanidine or cytosine (NNG or NNC), and this difference was conserved when comparisons were made between polyploid and diploid forms in both the cotton and wheat taxa. Preference for NNA/T codons was heterogeneous among genes with various numbers of introns and was also differential among the exons. SCUB patterns distinguished tetraploid cotton from its diploid progenitor species, as well as bread wheat from its diploid/tetraploid progenitor species, indicating that SCUB in the chloroplast genome partially mirrors the formation of polyploidies.

scholarly journals Characteristics of synonymous codon usage bias in the beginning region of West Nile virus

2014 ◽  
Vol 13 (3) ◽  
pp. 7347-7355 ◽  
Author(s):  
X.X. Ma ◽  
Y.P. Feng ◽  
J.L. Liu ◽  
L. Chen ◽  
Y.Q. Zhao ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
West Nile ◽  
In The Beginning ◽  
Synonymous Codon Usage Bias

scholarly journals Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates

VirusDisease ◽  
2017 ◽  
Vol 28 (2) ◽  
pp. 156-163 ◽  
Author(s):  
Atul B. Patil ◽  
Vijayendra S. Dalvi ◽  
Akhilesh A. Mishra ◽  
Bal Krishna ◽  
Abdul Azeez
Keyword(s):  
Coat Protein ◽  
Codon Usage ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Codon Usage Bias ◽  
Protein Gene ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Virus Isolates ◽  
Synonymous Codon Usage Bias

scholarly journals Analysis of Synonymous Codon Usage Bias in Chlamydia

2005 ◽  
Vol 37 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Hui Lü ◽  
Wei-Ming Zhao ◽  
Yan Zheng ◽  
Hong Wang ◽  
Mei Qi ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Synonymous Codon Usage Bias

scholarly journals Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

2015 ◽  
Vol 11 ◽  
pp. EBO.S22566 ◽  
Author(s):  
Yueying Qi ◽  
Wenjing Xu ◽  
Tian Xing ◽  
Mingming Zhao ◽  
Nana Li ◽  
...  
Keyword(s):  
Codon Usage ◽  
Gene Structure ◽  
Codon Usage Bias ◽  
Plastid Genome ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Synonymous Codon Usage Bias

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects

2012 ◽  
Vol 23 (6) ◽  
pp. 447-460 ◽  
Author(s):  
C. Selva Kumar ◽  
Rahul R. Nair ◽  
K. G. Sivaramakrishnan ◽  
D. Ganesh ◽  
S. Janarthanan ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Aquatic Insects ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Synonymous Codon Usage Bias
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