Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L

Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence

BACKGROUND

Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, and medicinal components, there has been limited research on phylogenomics. To reveal their plastid genome characteristics and phylogenetic relationships, we sequenced and assembled the plastomes of all five Schnabelia species (S. oligophylla, S. tetrodonta, S. nepetifolia, S. terniflora, S. aureoglandulosa), conducted comparative genomic analyses, and constructed a phylogenetic tree incorporating closely related taxa in subfamily Ajugoideae, as well as conducting divergence time estimation.

RESULTS

Plastome size of the five species ranged from 155,733 bp to 156,944 bp, encompassing 115 unique genes, with a GC content of 37.8% same for all species. Five intergenic spacer regions (trnH-GUG-psbA, trnK-UUU-matK, petB-petD, ndhD-psaC, ndhA-ndhH) were identified as divergence hotspots. Gene selection pressure analysis demonstrated that all genes were under negative selection. Phylogenetic relationship of Ajugoideae species based on plastomes confirmed the monophyly of Schnabelia. Two clades within Schnabelia were supported, one containing two original species and the other comprising three species transferred from Caryopteris. The stem age of the Schnabelia is estimated to be approximately 30.24 Ma, with the split of two Sections occurring around 12.60 Ma.

CONCLUSIONS

We revealed plastid genome evolutionary features for five species within the genus Schnabelia. The identified highly variable regions can provide a tool for future identification of these medicinal plants. The diversification of Schnabelia during middle Miocene and the Quaternary suggests that historical geological and climatic shifts facilitated species differentiation. These findings enhance our understanding of Schnabelia's evolution and support future research on chloroplast diversity, aiding conservation and sustainable use.

Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification

Introduction

Meliaceae, a significant group in Sapindales, possesses material and medicinal value due to its applications in timber and bioactive compounds. However, the high morphological diversity of the Meliaceae species and the lack of comparative studies of chloroplast (cp) genomes have led to great challenges in the classification and identification of Meliaceae species.

Methods

In this study, we sequenced the complete cp genomes of three Toona species (Toona fargesii, Toona ciliata, and Toona sinensis), and conducted comparative analyses of these cp genomes along with 29 previously published cp genomes of Meliaceae. Additionally, we performed the phylogenetic analyses and estimated the divergence times of Meliaceae.

Results

The cp genomes of 32 Meliaceae species ranged from 158,558 bp to 160,978 bp in length. Specifically, the cp genomes of Toona varied from 159,242 bp to 159,617 bp in length. These cp genomes contained a total of 135 unique genes, comprising 90 protein-coding, 8 rRNA, and 37 tRNA genes. Divergence time estimation revealed that the Meliaceae family diverged into two subfamilies (Cedreloideae and Melioideae) approximately 72.92 Ma (95% HPD: 60.62-87.01 Ma) in the Late Cretaceous. The diversification of Cedreloideae (47.86 Ma, 95% HPD: 47.42-48.22 Ma) occurred later than that of Melioideae (66.60 Ma, 95% HPD: 55.41-79.73 Ma). Furthermore, comparative genomic analysis identified 52 to 116 simple sequence repeats (SSRs) and twelve highly variable regions (HVRs) found among the cp genomes of Meliaceae.

Discussion

Divergence time estimation indicates that most Meliaceae species have a relatively recent origin, with rapid divergence occurring during the Late Oligocene or Early Miocene epochs. Comparative analysis of cp genomes revealed that Meliaceae exhibits relative conservation in terms of cp genome size, inverted-repeat (IR) boundary, genome structure, HVRs and codon patterns. Although differences exist between the Cedreloideae and Melioideae subfamilies, the overall similarity remains notably high. Furthermore, the ycf1, trnK-rps16, and ndhF-rpl32 regions exhibited the highest nucleotide polymorphism within Meliaceae, while the rpl22 gene displayed significant genetic diversity within both subfamilies. As candidate molecular markers, these regions may effectively distinguish among species. These findings not only provide insights into the evolution and species identification but also establish a scientific foundation for future systematics within Meliaceae.

Analysis of the Codon Usage Bias Pattern in the Chloroplast Genomes of Chloranthus Species (Chloranthaceae)

BACKGROUND

The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientific importance in the application of chloroplast genetic engineering and the genetic improvement of species. Chloranthus, an ancestral angiosperm with significant economic, medicinal, and ornamental value, belongs to the basal angiosperms. However, the codon usage patterns among Chloranthus species have remained unclear.

METHODS

To investigate codon usage bias and its influencing factors in Chloranthus chloroplast genomes, we utilized CodonW, CUSP, and SPSS software to analyze the chloroplast genomes of seven Chloranthus species.

RESULTS

In this study, we reported and characterized the complete chloroplast genome of the Chinese endemic species Chloranthus angustifolius. The phylogenetic tree based on the whole chloroplast genomes showed that C. angustifolius is sister to Chloranthus fortunei, and the genus Chloranthus is divided into two major clades, consistent with previous studies. Our results revealed that the GC content at different codon positions across all seven Chloranthus species was less than 50%, with GC1 > GC2 > GC3. Additionally, the average effective number of codons (ENC) values exceeded 45. A total of 10 shared optimal codons were identified, nine of which end with A or U. PR2-plot, ENC-plot, and neutrality plot analyses indicated that natural selection primarily influenced codon usage bias in the chloroplast genomes of Chloranthus.

CONCLUSIONS

We newly obtained the chloroplast genome of C. angustifolius and proposed that natural selection played a key role in codon usage patterns in Chloranthus species. These findings contribute to our understanding of evolutionary history and genetic diversity within this genus.

Correlations of gene expression, codon usage bias, and evolutionary rates of the mitochondrial genome show tissue differentiation in Ophioglossum vulgatum

BACKGROUND

Mitochondria are crucial for energy production in plant tissues, but their quantity and activity vary in different tissues and developmental processes. Determining the factors underlying differential molecular evolutionary rates has long been a central question in evolutionary biology, with expression level emerging as the prime predictor. Although we have previously observed an anti-correlation between expression level (E) and evolutionary rate (R) in chloroplast genes, it remains unclear whether such an anti-correlation exists in plant mitochondrial genes. Ophioglossum vulgatum is a typical plant belonging to the Ophioglossaceae, characterized by its unique morphology with only a single leaf above ground. It holds significant scientific and medicinal value. Using the mitochondrial genome and transcriptome data of O. vulgatum, we first analyzed the correlation between mitochondrial gene expression, codon usage bias, and evolutionary rates in different tissues.

RESULTS

Our findings indicated that mitochondrial gene expression level was the strongest between stem and leaf, while the weakest was between sporangium and root. Kruskal-Wallis tests revealed significant differences across various tissue types. Codon usage bias was influenced by both mutation and selection, with selection exerting a greater impact. The Spearman's rank correlation coefficients between codon adaptation index and expression levels of sporangium, stem, leaf, and root were 0.1178, 0.3926, 0.4463, and 0.2945, respectively, with significance in stem and leaf (P < 0.05). The correlation coefficients between the nonsynonymous substitution rate (dN) and expression levels in sporangium, stem, leaf, and root were -0.0840, -0.1786, -0.1714, and -0.0857, respectively, yet none are statistically significant. The correlation coefficient between the synonymous substitution rate (dS) and expression levels in sporangium was negative, whereas those between dS and the stem, leaf, and root were positive, although they were not significant. The dN/dS ratio exhibited a significant negative correlation with expression levels in both leaf and root (P < 0.05).

CONCLUSIONS

For the first time, our study revealed differences in the correlation between mitochondrial gene expression and codon usage bias, as well as evolutionary rates, across various tissues of O. vulgatum. Moreover, we also provide novel insights into understanding the effects of plant mitochondrial gene expression on evolutionary patterns.

Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae)

Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of D. octopetala var. asiatica. The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of D. octopetala var. asiatica was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of D. octopetala var. asiatica.

Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression

Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full-length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression-modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra-transcribed region scale. The expMotif-transcribed region combination is the most predominant contributor to the expression-modulating effect of SSRs, and some intra-transcribed regions are critical for this effect. Genes containing the same type of expMotif-SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.

Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns

Genes with similar or related functions in chloroplasts are often arranged in close proximity, forming clusters on chromosomes. These clusters are transcribed coordinated to facilitate the expression of genes with specific function. Our previous study revealed a significant negative correlation between the chloroplast gene expression level of the rare medicinal fern Ophioglossum vulgatum and its evolutionary rates as well as selection pressure. Therefore, in this study, we employed a combination of SMRT and Illumina sequencing technology to analyze the full-length transcriptome sequencing of O. vulgatum for the first time. In particular, we experimentally identified gene clusters based on transcriptome data and investigated the effects of chloroplast gene clustering on expression and evolutionary patterns. The results revealed that the total sequenced data volume of the full-length transcriptome of O. vulgatum amounted to 71,950,652,163 bp, and 110 chloroplast genes received transcript coverage. Nine different types of gene clusters were experimentally identified in their transcripts. The chloroplast cluster genes may cause a decrease in non-synonymous substitution rate and selection pressure, as well as a reduction in transversion rate, transition rate, and their ratio. While expression levels of chloroplast cluster genes in leaf, sporangium, and stem would be relatively elevated. The Mann-Whitney U test indicated statistically significant in the selection pressure, sporangia and leaves groups (P < 0.05). We have contributed novel full-length transcriptome data resources for ferns, presenting new evidence on the effects of chloroplast gene clustering on expression land evolutionary patterns, and offering new theoretical support for transgenic research through gene clustering.

Organellar phylogenomics of Ophioglossaceae fern genera

Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.

Revealing Molecular Patterns of Alzheimer's Disease Risk Gene Expression Signatures in COVID-19 Brains

Background

Various virus infections are known to predispose to Alzheimer's disease (AD), and a linkage between COVID-19 and AD has been established. COVID-19 infection modulates the gene expression of the genes implicated in progression of AD.

Objective

Determination of molecular patterns and codon usage and context analysis for the genes that are modulated during COVID-19 infection and are implicated in AD was the target of the study.

Methods

Our study employed a comprehensive array of research methods, including relative synonymous codon usage, Codon adaptation index analysis, Neutrality and parity analysis, Rare codon analyses, and codon context analysis. This meticulous approach was crucial in determining the molecular patterns present in genes up or downregulated during COVID-19 infection.

Results

G/C ending codons were preferred in upregulated genes while not in downregulated genes, and in both gene sets, longer genes have high expressivity. Similarly, T over A nucleotide was preferred, and selection was the major evolutionary force in shaping codon usage in both gene sets. Apart from stops codons, codons CGU - Arg, AUA - Ile, UUA - Leu, UCG - Ser, GUA - Val, and CGA - Arg in upregulated genes, while CUA - Leu, UCG - Ser, and UUA - Leu in downregulated genes were present below the 0.5%. Glutamine-initiated codon pairs have high residual values in upregulated genes. Identical codon pairs GAG-GAG and GUG-GUG were preferred in both gene sets.

Conclusions

The shared and unique molecular features in the up- and downregulated gene sets provide insights into the complex interplay between COVID-19 infection and AD. Further studies are required to elucidate the relationship of these molecular patterns with AD pathology.

Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae)

The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.

Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes

Xyloglucan endotransglycosylase (XET) genes are widely distributed in most plants, but the codon usage bias of XET genes has remained uncharacterized. Thus, we analyzed the codon usage bias using 4500 codons of 20 XET genes to elucidate the genetic and evolutionary patterns. Phylogenetic and hierarchical cluster analyses revealed that the 20 XET genes belonged to two groups. The closer the genetic distance, the more similar the codon usage preference. The codon usage bias of most XET genes was weak, but there was also some codon usage bias. AGA, AGG, AUC, and GUG were the top four codons (RSCU > 1.5) in the 20 XET genes. CitXET had a stronger codon usage bias, and there were eight optimal codons of CitXET (i.e., AGA, AUU, UCU, CUU, CCA, GCU, GUU, and AAA). The RSCU values underwent a correspondence analysis. The two main factors affecting codon usage bias (i.e., Axes 1 and 2) accounted for 54.8% and 17.6% of the total variation, respectively. Multiple correspondence analysis revealed that XET genes were widely distributed, with Group 1 genes being closer to Axis 1 than Group 2 genes, which were closer to Axis 2. Codons with A/U at the third codon position were distributed closer to Axis 1 than codons with G/C at the third codon position. PgXET, ZmXET, VlXET, VrXET, and PcXET were biased toward codons ending with G/C. In contrast, CitXET, DpXET, and BrpXET were strongly biased toward codons ending with A/U, indicating that these XET genes have a strong codon usage bias. Translational selection and base composition (especially A and U at the third codon position), followed by mutation pressure and natural selection, may be the most important factors affecting codon usage of 20 XET genes. These results may be useful in clarifying the codon usage bias of XET genes and the relevant evolutionary characteristics.