Phylogeny and evolution of chloroplast tRNAs in Adoxaceae

Abstract

Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ‐stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences “U‐U‐x2‐C” and “U‐x‐G‐x2‐T,” thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

“…The molecular markers such as highly divergent regions and repeat sequences derived from the entire plastome sequence hold promise for use in species delimitation and population genetics [ 29 – 31 ]. Moreover, the comparison of complete plastome sequences further provides the opportunity to explore sequence variation and molecular evolutionary patterns associated with gene loss, rearrangements, duplication, and transfer events [ 32 – 34 ]. Until now, plastomes have only been used for comparative analyses of single species of Fagopyrum or a few species of the genus [ 35 , 36 ].…”

Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants

“…Phylogenetic analysis revealed that the introns in chloroplast tRNA Val of Gossypium populifolium and Zea mays aggregated to the same branch (Figure 3), suggesting that the introns of corn and cotton have a close phylogenetic relationship. Additionally, chloroplast tRNAs with introns were grouped with cyanobacteria, providing supportive evidence for a common cyanobacterial lineage source of cp tRNAs [58].…”

“…tRNA Leu and tRNA Ser were observed to have 80 nt or more. These two tRNA isotypes were also found to harbor more than 83 nt in Adoxaceae plants, which shows that the gene sequences of tRNA Ser and tRNA Leu are longer than other tRNAs [58]. In addition, some tRNA isoacceptors were not observed in the cp genome of Gossypium, which was similar to that of the species in Gramineae [28].…”

“…In this study, most of the involved tRNAs were observed to harbor the conservative sequence U-U-C-X3-U at their Ψ-loop (Table 3). Additionally, in Adoxaceae, U-U-C-A conservative nucleotides at its Ψ-loop region were found [58]. This showed that the short consensus sequences might be important components of the molecular recognizer in the Ψ-loop, and are associated with the recognition of ribosomal RNA during the translation process [62].…”

Plastome comparison and phylogenomic of Fagopyrum (Polygonaceae): insights into detailed sequence divergence and taxonomic relationships

“…The molecular markers such as highly divergent regions and repeat sequences derived from the entire plastome sequence hold promise for use in species delimitation and population genetics [29][30][31]. Moreover, the comparison of complete plastome sequences further provides the opportunity to explore sequence variation and molecular evolutionary patterns associated with gene loss, rearrangements, duplication, and transfer events [32][33][34]. Until now, plastomes have only been used for comparative analyses of single species of Fagopyrum or a few species of the genus.…”