Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events

Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species

Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination

Introduction

Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding.

Methods

A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.

Results

The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing.

Conclusion

In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant

Trichosanthes kirilowii (T. kirilowii) is a valuable plant used for both medicinal and edible purposes. It belongs to the Cucurbitaceae family. However, its phylogenetic position and relatives have been difficult to accurately determine due to the lack of mitochondrial genomic information. This limitation has been an obstacle to the potential applications of T. kirilowii in various fields. To address this issue, Illumina and Nanopore HiFi sequencing were used to assemble the mitogenome of T. kirilowii into two circular molecules with sizes of 245,700 bp and 107,049 bp, forming a unique multi-branched structure. The mitogenome contains 61 genes, including 38 protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Within the 38 PCGs of the T. kirilowii mitochondrial genome, 518 potential RNA editing sites were identified. The study also revealed the presence of 15 homologous fragments that span both the chloroplast and mitochondrial genomes. The phylogenetic analysis strongly supports that T. kirilowii belongs to the Cucurbitaceae family and is closely related to Luffa. Collinearity analysis of five Cucurbitaceae mitogenomes shows a high degree of structural variability. Interestingly, four genes, namely atp1, ccmFC, ccmFN, and matR, played significant roles in the evolution of T. kirilowii through selection pressure analysis. The comparative analysis of the T. kirilowii mitogenome not only sheds light on its functional and structural features but also provides essential information for genetic studies of the genus of Cucurbitaceae.

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.

De Novo Hybrid Assembly Unveils Multi-Chromosomal Mitochondrial Genomes in Ludwigia Species, Highlighting Genomic Recombination, Gene Transfer, and RNA Editing Events

Biological invasions have been identified as the fifth cause of biodiversity loss, and their subsequent dispersal represents a major ecological challenge. The aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) are largely distributed in aquatic environments in North America and in Europe. However, they also present worrying terrestrial forms that are able to colonize wet meadows. To comprehend the mechanisms of the terrestrial adaptation of Lgh and Lpm, it is necessary to develop their genomic resources, which are currently poorly documented. We performed de novo assembly of the mitogenomes of Lgh and Lpm through hybrid assemblies, combining short reads (SR) and/or long reads (LR) before annotating both mitogenomes. We successfully assembled the mitogenomes of Lgh and Lpm into two circular molecules each, resulting in a combined total length of 711,578 bp and 722,518 bp, respectively. Notably, both the Lgh and Lpm molecules contained plastome-origin sequences, comprising 7.8% of the mitochondrial genome length. Additionally, we identified recombinations that were mediated by large repeats, suggesting the presence of multiple alternative conformations. In conclusion, our study presents the first high-quality mitogenomes of Lpm and Lgh, which are the only ones in the Myrtales order found as two circular molecules.

The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome

Water hyacinth (Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, and temperature. The International Union for Conservation of Nature (IUCN) has listed P. crassipes among the top 100 invasive species. However, comprehensive genomic information, particularly concerning its mitochondrial genome (mitogenome), remains surprisingly limited. In this study, the complete mitogenome of P. crassipes was analyzed using bioinformatics approaches. The mitogenome is 399,263 bp long and contains 38 protein-coding genes (PCGs), 24 tRNA genes, and 3 rRNA genes. Sequence analysis revealed that the complete mitogenome of the species contains 3,289 dispersed repeats, and 765 RNA editing sites in protein-coding genes. The P. crassipes mitogenome possessed un-conserved structures, including extensive sequence transfer between its chloroplasts and mitochondria. Our study on the mitogenome of P. crassipes offers critical insights into its evolutionary patterns and phylogenetic relationships with related taxa. This research enhances our understanding of this invasive species, known for its significant biomass and rapid overgrowth in aquatic environments.

Mitochondrial genome variation and intergenomic sequence transfers in Hevea species

Among the Hevea species, rubber tree (Hevea brasiliensis) is the most important source of natural rubber. In previous studies, we sequenced the complete nuclear and chloroplast genomes of Hevea species, providing an invaluable resource for studying their phylogeny, disease resistance, and breeding. However, given that plant mitochondrial genomes are more complex and more difficult to assemble than that of the other organelles, little is known about their mitochondrial genome, which limits the comprehensive understanding of Hevea genomic evolution. In this study, we sequenced and assembled the mitochondrial genomes of four Hevea species. The four mitochondrial genomes had consistent GC contents, codon usages and AT skews. However, there were significant differences in the genome lengths and sequence repeats. Specifically, the circular mitochondrial genomes of the four Hevea species ranged from 935,732 to 1,402,206 bp, with 34-35 unique protein-coding genes, 35-38 tRNA genes, and 6-13 rRNA genes. In addition, there were 17,294-46,552 bp intergenomic transfer fragments between the chloroplast and mitochondrial genomes, consisting of eight intact genes (psaA, rrn16S, tRNA-Val, rrn5S, rrn4.5S, tRNA-Arg, tRNA-Asp, and tRNA-Asn), intergenic spacer regions and partial gene sequences. The evolutionary position of Hevea species, crucial for understanding its adaptive strategies and relation to other species, was verified by phylogenetic analysis based on the protein-coding genes in the mitochondrial genomes of 21 Malpighiales species. The findings from this study not only provide valuable insights into the structure and evolution of the Hevea mitochondrial genome but also lay the foundation for further molecular, evolutionary studies, and genomic breeding studies on rubber tree and other Hevea species, thereby potentially informing conservation and utilization strategies.

The first mitochondrial genome of Calophyllum soulattri Burm.f

Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.

Assembly and comparative analysis of the first complete mitochondrial genome of a traditional Chinese medicine Angelica biserrata (Shan et Yuan) Yuan et Shan

Duhuo, a member of the Angelica family, is widely used to treat ailments such as rheumatic pain. It possesses a diverse array of bioactivities, including anti-tumor, anti-inflammatory, and analgesic properties, as recent pharmacological research has revealed. Nevertheless, the mtDNA of Angelica species remains relatively unexplored. To address this gap, we sequenced and assembled the mtDNA of A. biserrata to shed light on its genetic mechanisms and evolutionary pathways. Our investigation indicated a distinctive multi-branched conformation in the A. biserrata mtDNA. A comprehensive analysis of protein-coding sequences (PCGs) across six closely related species revealed the presence of 11 shared genes in their mitochondrial genomes. Intriguingly, positive selection emerged as a significant factor in the evolution of the atp4, matR, nad3, and nad7 genes. In addition, our data highlighted a recurring trend of homologous fragment migration between chloroplast and mitochondrial organelles. We identified 13 homologous fragments spanning both chloroplast and mitochondrial genomes. The phylogenetic tree established a close relationship between A. biserrata and Saposhnikovia divaricata. To sum up, our research would contribute to the application of population genetics and evolutionary studies in the genus Acanthopanax and other genera in the Araliaceae family.

The mitochondrial genomes of Panax notoginseng reveal recombination mediated by repeats associated with DNA replication

Panax notoginseng is one of the most valuable medicinal species. However, its mitochondrial genome has not been reported yet. We aimed to determine the mitogenome sequence of P. notoginseng. We de novo assembled the mitogenome with Illumina short reads and Nanopore long reads. The mitochondrial genome of P. notoginseng has a multipartite structure consisting of interconversion between a "master circle" and numerous "subgenomic circles" through recombinations mediated by 64 pairs of repetitive sequences. Among the multipartite structure, seven subgenomic circles were best supported. Six of the seven subgenomic circles shared an 852 bp conserved fragment. The complete mitogenome of P. notoginseng was 662,479 bp long including 34 mitochondrial protein-coding genes (PCGs), three rRNA, and 19 tRNA genes. We identified 166 microsatellite repeats and 26 long-tandem repeats. Phylogenetic analysis resolved a tree that was mostly congruent with the phylogeny of Apiales species described in the APG IV system and the tree built with the chloroplast genome sequences. A total of 12 mitochondrial plastid DNA fragments were identified. Lastly, we predicted 591C-to-U RNA editing sites in the coding regions of mitochondrial PCGs. The mitochondrial genome will lay the foundation for understanding the evolution of Panax species.

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

BACKGROUND

Punica granatum is a fundamentally important fruit tree that has important economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study the P. granatum mitogenome was sequenced and assembled to further understanding of organization, variation, and evolution of mitogenomes of this tree species.

RESULTS

The genome structure was multi-chromosomes with seven circular contigs, measuring 382,774 bp in length with a 45.91% GC content. It contained 74 genes, including 46 protein-coding genes, 25 tRNA genes, and three rRNA genes. There were 188 pairs of dispersed repeats with lengths of 30 or greater, primarily consisting of reverse complementary repeats. The mitogenome analysis identified 114SSRs and 466 RNA editing sites. Analyses of codon usage, nucleotide diversity and gene migration from chloroplast to mitochondrial were also conducted. The collinear and comparative analysis of mitochondrial structures between P. granatum and its proximal species indicated that P. granatum 'Taishanhong' was closely related to P. granatum 'Qingpitian' and Lagerstroemia indica. Phylogenetic examination based on the mitogenome also confirmed the evolutionary relationship.

CONCLUSION

The results offered crucial information on the evolutionary biology of pomegranate and highlighted ways to promote the utilization of the species' germplasm.

Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing

Background

Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.

Results

We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution.

Conclusion

Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.