The uniparental inheritance and variable mutation rate of different regions of the chloroplast genome make it suitable for studies ranging from population genetics to phylogenetics 10, 11. It is prokaryotic in origin and shows uniparental inheritance-paternal in some gymnosperms and maternal in most angiosperms 7, 8, 9. The chloroplast is a vital organelle in plants due to its role in photosynthesis 6. The subfamily Asteroideae is the youngest and largest subfamily of Asteraceae, comprising more than 17,000 species 1, 4. Among these families, the four subfamilies Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae are considered core Asteraceae 5. This family is divided into 13 subfamilies, including Barnadesioideae, Famatinanthoideae, Stifftioideae, Mutisioideae, Gochnatioideae, Wunderlichioideae, Hecastocleidoideae, Pertyoideae, Carduoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae 1, 3, 4. These species are diverse in distributions and habitat, exist on every continent, including Antarctica, and occupy every type of habitat 1, 2. The Asteraceae family has between 25,000 and 35,000 species which is ~ 10% of flowering plants and comparable only to the Fabaceae and Orchidaceae families 1. The plant family Asteraceae (Compositae), commonly known as the daisy or sunflower family, is among the three megadiverse families that comprise up to 25% of angiosperm species 1. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA ( trnT-UGU) decodes all four codons of threonine. Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5′ acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species.
The pseudogenization of the chloroplast threonine ( trnT -GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae).
Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The chloroplast genome evolves through the course of evolution.
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