Comparative Genomics of <i>Triticum, Secale,</i> and <i>Triticale</i>: Codon Usage Bias in Chloroplast Genomes and Its Implications for Evolution and Genetic Engineering.

ABSTRACT: Chloroplast codon usage bias (CUB) records both maternal phylogeny and selection intensity. Characterizing CUB in the synthetic cereal × Triticosecale and its Triticum and Secale parents is therefore a prerequisite for plastid-based engineering and for tracing the evolutionary consequences of recent allopolyploidy. Complete plastome sequences of five taxa-Triticum monococcum, T. turgidum, T. aestivum, Secale cereale and × Triticosecale sp.-were downloaded. Protein-coding genes were extracted to calculate overall GC, GC1-GC3, SCUO, RSCU, ENC-GC3s, neutrality, and PR2 plots. Optimal codons were defined as RSCU ≥ 1 and △RSCU ≥ 0.8. The results showed that the chloroplast genomes of these five species are low in GC content for the third base of codons, suggesting an end preference for A

SUBMITTER: Tian T 

PROVIDER: S-EPMC12610814 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature