Codon usage bias and determining forces in green plant mitochondrial genomes

Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata

BACKGROUND

Floating bamboo (Hygroryza aristata) is an endangered species with a narrow native distribution and is renowned for its unique aesthetic qualities, which holds significant ecological and ornamental value. However, the lack of genetic information research, with only one complete plastome available, significantly hampers conservation efforts and further research for this species.

RESULTS

In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade.

CONCLUSIONS

We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.

Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L

Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and patterns of evolution and mutation remain largely unexplored. This study examines the chloroplast genome, phylogeny, codon usage bias, and divergence time of C. officinalis, enhancing our understanding of its evolution and adaptation. The chloroplast genome of C. officinalis is a 150,465 bp circular molecule with a G + C content of 37.75% and comprises 131 genes. Phylogenetic analysis revealed a close relationship between C. officinalis, C. arvensis, and Osteospermum ecklonis. A key finding is the similarity in codon usage bias among these species, which, coupled with the divergence time analysis, supports their close phylogenetic proximity. This similarity in codon preference and divergence times underscores a parallel evolutionary adaptation journey for these species, highlighting the intricate interplay between genetic evolution and environmental adaptation in the Asteraceae family. Moreover unique evolutionary features in C. officinalis, possibly associated with certain genes were identified, laying a foundation for future research into the genetic diversity and medicinal value of C. officinalis.

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

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.

Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa

Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Introduction

Codon basis is a common and complex natural phenomenon observed in many kinds of organisms.

Methods

In the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.

Results

The results showed that the codons of all Amanita species tended to end in A/T, demonstrating the preference of mitochondrial codons of Amanita species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of Amanita is 30.81, which is <35, demonstrating the strong codon preference of mitochondrial core PCGs of Amanita. The neutrality plot analysis and PR2-Bias plot analysis further demonstrated that natural selection plays an important role in Amanita codon bias. In addition, we obtained 5–10 optimal codons (ΔRSCU > 0.08 and RSCU > 1) in nine Amanita species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different Amanita species and found large variations between them.

Discussion

This study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.

Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae)

To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnS^GCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.

Free energy of mRNA positively correlates with GC content in chloroplast transcriptomes of edible legumes

In the present study, the results of nucleotide composition analysis showed that the legume chloroplast (cp) transcriptomes were AT rich. From the neutrality plot, we observed that natural selection might have played a major role, while mutation pressure played a minor role in the CUB of cp transcriptomes. Highly significant (p < 0.05) negative correlation was found between mRNA free energy (mFE) and scaled chi-square for entire mRNA in Cicer arietinum and Lens culinaris suggesting that the release of higher energy by entire mRNA molecule might be associated with higher degree of codon usage bias in these two crop plants. Further, highly significant (p < 0.01, p < 0.05) positive correlation of mFE for entire mRNA was found with GC3 and that of mFE for 39 bases with GC, GC1, GC2 and GC3 contents among all the legumes. This indicated that higher GC content might induce the release of more free energy by cp transcriptomes.

Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species

The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.

Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.