Chloroplast Genome Research Articles

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

The genome sequence of the corn cockle, Agrostemma githago L., 1753 (Caryophyllaceae)

We present a genome assembly from an individual Agrostemma githago (the corn cockle; Tracheophyta; Magnoliopsida; Caryophyllales; Caryophyllaceae). The genome sequence has a total length of 1,735.0 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules suggesting the individual is a tetraploid (2n = 4x = 48). The organelle genomes have been assembled, and the length of the mitochondrial genome is 262.91 and the plastid genome 151.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 38,816 protein-coding genes.

A new computational method to estimate adaptation time in Avicennia by using divergence time

Evolutionary studies of plant groups which are distributed in vast geographical regions and face different ecological and environmental conditions are important as they through light on different mechanisms of local adaptation and species divergence through time. The genus Avicennia is one of these plant groups which inspire of few species show interesting geographical distribution with some degree of species-specific geographical isolations. In general, very limited molecular phylogenetic investigations have been carried out in the genus Avicennia, and therefore we conducted the present study with the following aims:To estimate the species divergence time based on different nuclear and chloroplast DNA regions, separately. This will illustrate how different genetic regions evolved in this genus,To identify the sequences with potential adaptive value against geographical variable by latent factor mixed models (LFMM) analysis,To illustrate the phylogenetic signal of these DNA regions and their role in speciation within the genus and,To introducing a new computational strategy for estimating adaptive time for the sequences. The results showed that different genetic regions may produce different species divergent time, both the nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast DNA sequences, contained potentially adaptive single nucleotide polymorphisms (SNPs).We could present a suggestive time for these adaptive sequences for the first time. In conclusion both local adaptation and independent mutations seem to have played role in Avicennia speciation and evolution.

The genome sequence of fat-hen, Chenopodium album L.

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2n = 6x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

The genome sequence of lesser burdock, Arctium minus (Hill) Bernh. (Asteraceae)

We present a genome assembly of a diploid specimen of Arctium minus (lesser burdock; Tracheophyta; Magnoliopsida; Asterales; Asteraceae). The genome sequence is 1,903.1 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 312.58 kilobases and 152.71 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,734 protein-coding genes.

Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae)

BackgroundLithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome.ResultsThe phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization.ConclusionsThis study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae.

From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation

BackgroundPlastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light.ResultsIn this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture.ConclusionWe newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.

Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species

(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, finding extensive use in forestry and landscape design across China. (2) Methods: This study employed Illumina’s second-generation sequencing technology to sequence the chloroplast genomes of eight Phyllostachys species, followed by their assembly and annotation. (3) Results: The chloroplast genomes of the genus exhibit a characteristic tetrad structure with an average sequence length of 139,699 bp and an average GC content of 38.9%. A total of 130 genes have been annotated across eight bamboo species, comprising 75 protein-coding genes, 28 tRNA genes, and four rRNA genes. Global alignment and nucleotide polymorphism analyses indicate that the chloroplast genome of Phyllostachys is highly conserved overall. The boundaries of the four chloroplast regions are relatively conserved and exhibit minimal differences. Among these regions, three coding region genes—atpH, trnQ-UUG, and petB—and five non-coding regions—rpl32-trnL-UAG, rpl14-rpl16, rpl22-rps19, rps12-clpP, and trnR-UCU-trnM-CAU—exhibit high polymorphism and can be used as potential hotspot areas for subsequent research. A total of 266 simple sequence repeat (SSR) loci were identified by SSR analysis in the chloroplast genomes of eight bamboo species; the largest number of mononucleotide repeats was 154, predominantly consisting of A/T. Codon bias in the chloroplast genomes of the eight bamboo species indicates a preference for codons ending with A and U. Additionally, the UUA codon, which encodes leucine (Leu), is positioned between codons encoding phenylalanine (Phe), lysine (Lys), leucine (Leu), serine (Ser), and tyrosine (Tyr), indicating certain differences among these species. (4) Conclusions: This study aims to offer novel insights into the population genetics, phylogenetic relationships, and evolutionary patterns of Phyllostachys.

The genome sequence of common reed, Phragmites australis (Cav.) Steud. (Poaceae)

We present a genome assembly from an individual Phragmites australis (the common reed; Streptophyta; Magnoliopsida; Poales; Poaceae). The genome sequence has a total length of 848.70 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2n = 4x = 48). The three mitochondrial assemblies had lengths of 304.58, 92.24, and 76.54 kilobases and the plastid genome assembly had a length of 137.67 kilobases. Gene annotation of this assembly on Ensembl identified 47,513 protein-coding genes.

Gastrochilusbalangshanensis (Orchidaceae, Aeridinae), a new subalpine epiphytic orchid from the Mountains of Southwest China.

Gastrochilusbalangshanensis, a new orchid species from the Balang Mountain, Sichuan Province, Southwest China, is described and illustrated. It morphologically resembles G.affinis, but differs in having shorter stems, a reniform epichile and a sub-hemispherical hypochile (spur), obtuse-rounded at the apex. The results of molecular phylogenetic analyses based on nuclear ribosome internal transcribed spacer (nrITS) and four chloroplast DNA markers (matK, psbA-trnH, psbM-trnD and trnL-F) from 50 Gastrochilus species indicate that G.balangshanensis is closely related to G.heminii and G.bernhardtianus, also endemic to the Hengduan Mountains. The novelty is a branch and trunk epiphyte in mixed coniferous forest.

A Pleistocene legacy of gene pools, ecodemes and admixtures of Stuckenia pectinata (L.) Börner as evidenced from microsatellites, complete chloroplast genomes and ribosomal RNA cistron (Europe, Africa)

Stuckenia pectinata (L.) Börner is a widely distributed submerged plant well-studied for its ecology, distribution, and molecular diversity. Globally, various genotypic lineages and hybrids of Stuckenia species have been identified using nuclear rRNA (ITS) and chloroplast sequences (notably rpl20–5’rps12 and trnT-trnL). These studies have shown intraspecific variability in S. pectinata, with two gene pools ('genotype 1a' and '1b') reported for Europe and Africa. Moreover, former isozyme research suggested distinct freshwater and brackish water gene pools. Therefore, our primary objective was to determine whether these ecodemes correspond to either 'genotype 1a' or '1b'. Using fifteen nuclear microsatellite loci, complete chloroplast genome sequences (156,677 bp), and the rRNA cistron (7178 bp), we analyzed the genetic identity of 313 S. pectinata samples (representing 124 unique clones) from 12 populations in Europe and Africa. Chloroplast genomes of three African Rift lake populations corresponded to ‘genotype 1b’, while those of nine European populations to ‘genotype 1a’. Microsatellites also clearly distinguished ‘genotype 1a’ from ‘1b’ in an individual PCoA and STRUCTURE analysis, whereas incomplete homogenization of 5S-rRNA sequences suggested either ongoing differentiation or intraspecific hybridization between ‘genotype 1a’ and ‘1b’. Haplotype lineages, rRNA cistron mutations, and microsatellites revealed an additional subdivision within ‘genotype 1a’, potentially distinguishing a freshwater gene pool from a brackish water one. Approximate Bayesian computation analyses using nuclear microsatellites supported a demographic expansion model and a time of divergence, for the African Rift lake populations as well as for the European freshwater and brackish water populations, dating back to the Late Pleistocene. Divergent chloroplast lineages appeared to be already present during the Last Glacial Maximum. Stuckenia pectinata from Lake Hora (Ethiopia), Lake Balaton (Hungary) and the Camargue (France) each harbored two distinct maternal haplotypes, from Selinunte (Italy) indicated F1 hybrids whereas from Lake Peipsi (Estonia), amongst others, showed incomplete rRNA homogenization. It is hypothesized that contemporary S. pectinata populations, especially in Europe, retained a legacy of ancient gene pool differentiation despite a history of hybridization, admixture, and chloroplast capture. It is recommended that studies on the ecology and reproductive strategies of this seemingly common and widespread species should take into account its genetic identity.

The genome sequence of the Black Medic, Medicago lupulina L.

We present a genome assembly from a specimen of Black Medic, Medicago lupulina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 575.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 294.12 kilobases and 123.99 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,424 protein-coding genes.

Comparative analysis of codon usage patterns in 16 chloroplast genomes of suborder Halimedineae.

The Halimedineae are marine green macroalgae that play crucial roles as primary producers in various habitats, including coral reefs, rocky shores, embayments, lagoons, and seagrass beds. Several tropical species have calcified thalli, which contribute significantly to the formation of coral reefs. In this study, we investigated the codon usage patterns and the main factors influencing codon usage bias in 16 chloroplast genomes of the suborder Halimedineae. Nucleotide composition analysis revealed that the codons of these species were enriched in A/U bases and preferred to end in A/U bases, and the distribution of GC content followed a trend of GC1 > GC2 > GC3. 30 optimal codons encoding 17 amino acids were identified, and most of the optimal codons and all of the over-expressed codons preferentially ended with A/U. The neutrality plot, effective number of codons (ENc) plot, and parity rule 2 (PR2) plot analysis indicated that natural selection played a major role in shaping codon usage bias of the most Halimedineae species. The genetic relationships based on their RSCU values and chloroplast protein-coding genes showed the closely related species have similar codon usage patterns. This study describes, for the first time, the codon usage patterns and characterization of Halimedineae chloroplast genomes, and provides new insights into the evolution of this suborder.

Complete chloroplast genomes of Desmidorchis penicillata (Deflers) plowes and Desmidorchis retrospiciens Ehrenb.: comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis.

The genome sequence of the common alder, Alnus glutinosa (L.) Gaertn. (Betulaceae)

We present a genome assembly of a diploid specimen of Alnus glutinosa (the common alder; Streptophyta; Magnoliopsida; Fagales; Betulaceae). The genome sequence has a total length of 456.80 megabases. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome assemblies have lengths of 505.23 and 155.85 kilobases and the plastid genome is 160.82 kilobases long. Gene annotation of this assembly on Ensembl identified 23,728 protein-coding genes.

Deciphering the multi- partite mitochondrial genome of Crataegus pinnatifida: insights into the evolution and genetics of cultivated Hawthorn

Flowering plant (angiosperm) mitochondrial genomes are remarkably dynamic in their structures. We present the complete mitochondrial genome of hawthorn (Crataegus pinnatifida Bunge), a shrub that bears fruit and is celebrated for its extensive medicinal history. We successfully assembled the hawthorn mitogenome utilizing the PacBio long-read sequencing technique, which yielded 799,862 reads, and the Illumina novaseq6000 sequencing platform, which producing 6.6 million raw paired reads. The C. pinnatifida mitochondria sequences encompassed a total length of 440,295 bp with a GC content of 45.42%. The genome annotates 54 genes, including 34 that encode proteins, 17 that encode tRNA, and three genes for rRNA. A fascinating interplay was observed between the chloroplast and mitochondrial genomes, which share 17 homologous sequences sequences that rotal 1,933 bp. A total of 134 SSRs, 22 tandem repeats and 42 dispersed repeats were identified in the mitogenome. Four conformations of C. pinnatifida mitochondria sequences recombination were verified through PCR experiments and Sanger sequencing, and C. pinnatifida mitogenome is more likely to be assembled into three circular-mapping chromosomes. All the RNA editing sites that were identified C-U edits, which predominantly occurred at the first and second positions of the codons. Phylogenetic and collinearity analyses identified the evolutionary trajectory of C. pinnatifida, which reinforced the genetic identity of the hawthorn section. This unveiling of the unique multi-partite structure of the hawthorn mitogenome offers a foundational reference for future study into the evolution and genetics of C. pinnatifida.

The genome sequence of Inga laurina (Sw.) Willd.

We present a genome assembly from an individual of Inga laurina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 899.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, supporting the individual being an autotetraploid with 2n=4x=52. The mitochondrial and plastid genome assemblies have lengths of 1,261.88 kilobases and 176.27 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,101 protein-coding genes.

The Complete Chloroplast Genome of Meconopsis simplicifolia and Its Genetic Comparison to Other Meconopsis Species.

Background: Chloroplasts, due to their high conservation and lack of recombination, serve as important genetic resources for the classification and evolutionary analysis of closely related species that are difficult to distinguish based on their morphological features. Meconopsis simplicifolia (M. simplicifolia), an endangered herb within the Meconopsis genus, has demonstrated therapeutic potential in treating various diseases. However, the highly polymorphic morphology of this species poses a challenge for accurate identification. Methods: In this study, the complete chloroplast genome of M. simplicifolia was sequenced and assembled using Illumina sequencing technology. Simple sequence repeats (SSRs) and repetitive sequences were characterized. In addition, a comparative analysis was conducted with the chloroplast genomes of six other Meconopsis species. Results: The chloroplast genome of M. simplicifolia has a quadripartite circular structure with a total length of 152,772 bp. It consists of a large single-copy region of 83,824 bp and a small single-copy region of 17,646 bp, separated by a pair of inverted repeat sequences (IRa and IRb, 25,651 bp). The genome contains 131 genes, 33 SSRs, and 27 long repetitive sequences. Comparative analysis with six other chloroplast genomes of Meconopsis revealed that M. simplicifolia is closely related to M. betonicifolia and that the rpl2 (ribosomal protein L2) gene in the IRb region has been deleted. This deletion is of significant importance for future taxonomic studies of M. simplicifolia. Conclusions: This study provides a valuable reference for the identification of M. simplicifolia and contributes to a deeper understanding of the phylogeny and evolution of the Meconopsis genus.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study.

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

The mitochondrial genome of Lavandula angustifolia Mill. (Lamiaceae) sheds light on its genome structure and gene transfer between organelles

BackgroundLavandula angustifolia holds importance as an aromatic plant with extensive applications spanning the fragrance, perfume, cosmetics, aromatherapy, and spa sectors. Beyond its aesthetic and sensory applications, this plant offers medicinal benefits as a natural herbal remedy and finds use in household cleaning products. While extensive genomic data, inclusive of plastid and nuclear genomes, are available for this species, researchers have yet to characterize its mitochondrial genome. This gap in knowledge hampers deeper understanding of the genome organization and its evolutionary significance.ResultsThrough the course of this study, we successfully assembled and annotated the mitochondrial genome of L. angustifolia, marking a first in this domain. This assembled genome encompasses 61 genes, which comprise 34 protein-coding genes, 24 transfer RNA genes, and three ribosomal RNA genes. We identified a chloroplast sequence insertion into the mitogenome, which spans a length of 10,645 bp, accounting for 2.94% of the mitogenome size. Within these inserted sequences, there are seven intact tRNA genes (trnH-GUG, trnW-CCA, trnD-GUC, trnS-GGA, trnN-GUU, trnT-GGU, trnP-UGG) and four complete protein-coding genes (psbA, rps15, petL, petG) of chloroplast derivation. Additional discoveries include 88 microsatellites, 15 tandem repeats, 74 palindromic repeats, and 87 forward long repeats. An RNA editing analysis highlighted an elevated count of editing sites in the cytochrome c oxidase genes, notably ccmB with 34 editing sites, ccmFN with 32, and ccmC with 29. All protein-coding genes showed evidence of cytidine-to-uracil conversion. A phylogenetic analysis, utilizing common protein-coding genes from 23 Lamiales species, yielded a tree with consistent topology, supported by high confidence values.ConclusionsAnalysis of the current mitogenome resource revealed its typical circular genome structure. Notably, sequences originally from the chloroplast genome were found within the mitogenome, pointing to the occurrence of horizontal gene transfer between organelles. This assembled mitogenome stands as a valuable resource for subsequent studies on mitogenome structures, their evolution, and molecular biology.