Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina

Abstract

Background: Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina.

Results: Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships.

Conclusions: There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.

Keywords: Codon usage bias; Hemerocallis citrina Baroni; Mitochondrial genome; Phylogeny.

Fig. 1

Correlation analysis of codon parameters in the H. citrina mitogenome. *, ** indicate correlations significant at the 0.05 and 0.01 levels, respectively

Fig. 2

ENC-plot analysis of the H. citrina mitogenome

Fig. 3

Distribution of ENC frequency of the H. citrina mitogenome

Fig. 4

Neutrality plot analysis of the H. citrina mitogenome

Fig. 5

PR2-plot analysis of the H. citrina mitogenome

Fig. 6

Heat map of codon usage preference based on RSCU values in the H. citrina mitogenome

Fig. 7

Clustering lineage plot based on RSCU values of the 15 monocotyledonous mitogenomes

Fig. 8

Phylogenetic tree based on the mt PCG for 15 monocot species