Codon use and the rate of divergence of land plant chloroplast genes - PubMed (original) (raw)

Comparative Study

Codon use and the rate of divergence of land plant chloroplast genes

B R Morton. Mol Biol Evol. 1994 Mar.

Abstract

Codon fitnesses for chloroplast genes were estimated using the relative synonymous codon use of psbA, which has a different pattern of codon use than other chloroplast genes and is the major translation product of the chloroplast. These estimates were used to calculate the codon adaptation index (CAI) of chloroplast genes from Marchantia polymorpha, Nicotiana tabacum, and Chlamydomonas reinhardtii. The genes with the highest CAI values in M. polymorpha correspond to those that are expressed at the highest levels. The rate of divergence between M. polymorpha and both C. reinhardtii and N. tabacum is inversely related to the CAI value of the M. polymorpha gene. The data suggest that selection is acting on the synonymous codon use of the highly expressed genes of the M. polymorpha chloroplast genome. The data set is inconclusive about N. tabacum genes, but, as there is a weaker correspondence between CAI value and expression level, it suggests that selection is not operating in this lineage.

PubMed Disclaimer

Cited by

Complete chloroplast genome sequence of Amomum villosum and comparative analysis with other Zingiberaceae plants.
Yang L, Feng C, Cai MM, Chen JH, Ding P. Yang L, et al. Chin Herb Med. 2020 Sep 16;12(4):375-383. doi: 10.1016/j.chmed.2020.05.008. eCollection 2020 Oct. Chin Herb Med. 2020. PMID: 36120171 Free PMC article.
Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family.
Du Q, Li J, Wang L, Chen H, Jiang M, Chen Z, Jiang C, Gao H, Wang B, Liu C. Du Q, et al. Planta. 2022 Sep 9;256(4):73. doi: 10.1007/s00425-022-03987-z. Planta. 2022. PMID: 36083348
Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences.
Kaya S, Çıplak B. Kaya S, et al. Heliyon. 2018 Nov 23;4(11):e00929. doi: 10.1016/j.heliyon.2018.e00929. eCollection 2018 Nov. Heliyon. 2018. PMID: 30519651 Free PMC article.
Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable.
Liu X, Zhou B, Yang H, Li Y, Yang Q, Lu Y, Gao Y. Liu X, et al. Molecules. 2018 Jun 5;23(6):1358. doi: 10.3390/molecules23061358. Molecules. 2018. PMID: 29874832 Free PMC article.
Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.
Liu X, Li Y, Yang H, Zhou B. Liu X, et al. Molecules. 2018 Apr 9;23(4):857. doi: 10.3390/molecules23040857. Molecules. 2018. PMID: 29642545 Free PMC article.

Codon use and the rate of divergence of land plant chloroplast genes - PubMed (original) (raw)