Aug 2026· Life· Vol 16, pp. 1391· 0 citations· 45 references
TL;DR
This study sequenced, assembled, and analyzed the complete mitochondrial genome of Rhodymenia intricata to investigate its genome organization, gene content, and phylogenetic position within Rhodymeniales, providing new insights into mitogenome evolution and phylogenetic relationships in red algae.
Abstract
Red algae (Rhodophyta) are an ancient lineage of photosynthetic eukaryotes that play important roles in marine ecosystems. However, genomic information for many species within the order Rhodymeniales remains limited, particularly for mitochondrial genomes. In this study, we sequenced, assembled, and analyzed the complete mitochondrial genome (mitogenome) of Rhodymenia intricata to investigate its genome organization, gene content, and phylogenetic position within Rhodymeniales. The mitogenome of R. intricata is a circular DNA molecule of 26,213 bp containing 49 genes, including 25 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes. The genome shows a strong A + T bias (70.9%) and positive AT and GC skews, typical of red algal mitogenomes. Comparative analysis with other Rhodymeniales mitogenomes revealed generally conserved gene content and organization, with several lineage-specific features such as the presence of the rpl20 gene, an additional open reading frame (orf148), and three rRNA genes (rnl, rns, and rns5). Codon usage analysis indicated a preference for leucine and isoleucine codons and dominant start and stop codons (ATG and TAA). Phylogenetic analysis based on a concatenated dataset of 23 mitochondrial PCGs strongly supported the monophyly of Rhodymeniales and confirmed the close relationship between R. intricata and R. pseudopalmata. Overall, this study presents the first complete mitogenome of R. intricata and expands mitogenomic resources for Rhodymeniales, providing new insights into mitogenome evolution and phylogenetic relationships in red algae.
Organelle genomes offer a powerful tool for red algal evolutionary studies. Although the number of Rhodophyta genomes has increased substantially over the past 2 decades, only two mitochondrial genomes have been reported for the red algal order Thoreales. In this study, we generated 10 new complete mitochondrial genomes of Thoreales, representing the order's two genera and eight species, which, combined with additional mitogenomes of related orders of the subclass Nemaliophycidae, resulted in a comprehensive dataset of 20 mitogenomes. Thoreales mitogenomes exhibited little variation, ranging in length from 25,022 bp to 26,369 bp, with GC content from 25.6% to 28.3%, gene numbers from 46 to 54, and protein-coding genes from 21 to 25. Four genes were missing in one or more species (atp4, rpl20, sdh2, and sdh4), and no introns were detected. Synteny among members of Thoreales was highly conserved and similar to other orders of Nemaliophycidae. Phylogenomic analyses strongly supported the monophyly of Thoreales within Nemaliophycidae. Within the order, Nemalionopsis and Thorea as well as the relationship among the species received full support. Nemalionopsis shawii and N. parkeri formed an early-diverging clade that was sister to Thorea, which had species that resolved into two distinct lineages lacking evident geographic or morphological differentiation. By expanding the available dataset from two to 10 mitogenomes, this study provides a broad organellar perspective on Thoreales evolution, contributing to new insights into the systematics and diversification of freshwater red algae and, potentially, for clarifying inter-ordinal relationships within Nemaliophycidae.
M. O. Paiano, Morgan I. Vis, Nadia M Lemes da Silva et al.· Journal of Phycology· 0 citations
BACKGROUND
Krascheninnikovia arborescens is a drought-tolerant subshrub of the Amaranthaceae family that is endemic to China and plays an important role in desert ecosystems. However, little is known about the structure and evolutionary dynamics of its organellar genomes. In this study, we assembled and characterized the mitochondrial and chloroplast genomes of K. arborescens using long-read sequencing data.
RESULTS
The mitochondrial genome was assembled as a master circular genome representation of 387,891 bp and contains 62 annotated genes, whereas the chloroplast genome exhibits a typical quadripartite structure of 152,039 bp with 90 genes. The mitochondrial genome harbors abundant repetitive sequences and multiple plastid-derived insertions, indicating a dynamic structural organization. In contrast, gene content remains highly conserved, and all core protein-coding genes show signatures of purifying selection, particularly those involved in ATP synthesis and respiratory metabolism. Predicted RNA editing sites differ substantially between the two organelles, suggesting distinct post-transcriptional modification patterns. Phylogenetic analyses based on shared organellar genes consistently place K. arborescens within Amaranthaceae and support its evolutionary relationships within Caryophyllales. These results reveal a combination of structural dynamism and functional conservation in the organellar genomes of K. arborescens.
CONCLUSION
This study provides a foundation for future comparative and evolutionary studies of Amaranthaceae and expands genomic resources for this family.
Limeum is the sole genus of Limeaceae, comprising approximately 20 species distributed across Africa, Southwest Asia, and India. However, genomic resources for the family are limited, and phylogenetic relationships within the genus remain poorly understood. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of six Limeum species to investigate their genomic characteristics and phylogenetic relationships. The chloroplast genomes ranged from 156,354 bp to 160,377 bp in length and exhibited the typical quadripartite structure. Each genome contained 131 genes, consisting of 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analyses identified 455 tandem repeats and 616 simple sequence repeats, revealing 16 highly variable regions that may serve as potential molecular markers for future studies. Phylogenetic analyses based on complete chloroplast genome sequences strongly supported the monophyly of Limeum and robustly resolved interspecific relationships within the genus. These results provide the first comprehensive plastome dataset for Limeum and a valuable genomic resource for species identification, genetic diversity assessment, phylogenetic reconstruction, and evolution studies of Limeum and the family Limeaceae.
Zheng-Lin He, Jin-Fei Xiao, Fei Zhao et al.· Korean Journal of Plant Taxo...· 0 citations
The family Epialtidae is the most species-rich lineage within the superfamily Majoidea, but complete mitochondrial genomes (mitogenomes) have been reported for only a few of its members. In this study, we sequenced the complete mitogenome of the decorator crab
Hyastens ducator
using next-generation high-throughput sequencing, annotated its mitochondrial genes and analysed its genomic organisation. The complete mitogenome of
H. ducator
is 15 894 bp in length and contains 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes and 22 transfer RNA genes. The tRNAs range from 52 to 74 bp in length. The nucleotide composition of the complete mitogenome is 34.9% A, 18.2% C, 9.4% G and 37.5% T. A comparison of gene order among species within Majoidea shows that the overall gene order of mitogenomes is largely conserved, but the positions of some short genes and non-coding regions vary to different degrees. Most changes occur in transfer RNA regions and gene orders ranged from highly conserved to extensively rearranged among different lineages. Phylogenetic analyses based on the 13 PCGs robustly placed
H. ducator
within Epialtidae, clustered it with other epialtid species with strong support and provided new molecular evidence for relationships among families and genera within Majoidea. Overall, this study reports the mitogenome of
H. ducator
for the first time, clarifies its phylogenetic position, enriches the molecular dataset for the family Epialtidae and provides an important reference for future taxonomic and evolutionary studies of Majoidea.
Chenfang Niu, Jichun Li, Yingxuan Bao et al.· Crustaceana· 0 citations
Abstract The genus Acanthaspis (Hemiptera: Reduviidae) comprises predatory insects of ecological importance, yet mitochondrial genomic resources for this group remain limited. Here, we present the complete mitochondrial genome of Acanthaspis geniculata (Hsiao, 1976). The mitogenome is 16,226 bp in length and contains the standard set of 37 mitochondrial genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes), along with a control region (D-loop). The nucleotide composition is A (40.4%), T (29.6%), C (17.9%), and G (12.1%), with an overall AT content of 70.0%. Phylogenetic analyses based on partitioned mitochondrial datasets strongly support the monophyly of the subfamily Reduviinae and reveal that A. geniculata forms a close sister-group relationship with A. ruficeps and A. pedestris. This study provides a fundamental mitogenomic resource for future evolutionary and systematic studies of the Reduviidae.
Wan-Ting Liu, Jia-Hao Chen, Jia-Kun Lin et al.· Mitochondrial DNA Part B: Re...· 0 citations
Introduction Rhodiola juparensis, a cushion plant, plays a critical role in sustaining the fragile ecological environment of the Qinghai‑Tibet Plateau. Understanding its adaptive evolution is essential, yet the organelle genomic architecture and evolutionary dynamics of this species remain poorly characterized. Methods We sequenced and assembled the chloroplast (plastome) and mitochondrial (mitogenome) genomes of R. juparensis. Comprehensive comparative analyses were performed on organellar genome structure, RNA editing events, and positively selected genes. Divergence time estimation and genome‑wide positive selection scans were conducted using phylogenetic and bioinformatic approaches. Results The plastome exhibited a more conserved structure but a faster nucleotide substitution rate, whereas the mitogenome showed greater structural complexity but a slower substitution rate. Divergence time estimation suggested that rapid differentiation of Crassulaceae species occurred around 7.15 Mya, likely linked to decreasing atmospheric CO₂ levels and the dramatic uplift of the Qinghai‑Tibet Plateau during the Late Miocene. Positive selection analysis identified three candidate genes (matR, ccmFc, and ATP8) under positive selection. Additionally, numerous pentatricopeptide repeat (PPR) proteins were detected in the nuclear genome. Discussion The contrasting evolutionary patterns between the two organellar genomes highlight distinct selective constraints and mutation rates. The identified positively selected genes may contribute to mitochondrial function and stress adaptation. The abundance of nuclear‑encoded PPR proteins suggests a potential repair mechanism via RNA editing that could mitigate UV‑induced DNA damage, offering an adaptive advantage in the high‑altitude environment. Collectively, these findings provide valuable insights into the adaptive evolution of R. juparensis and the evolutionary history of Crassulaceae on the Qinghai‑Tibet Plateau.
Guocui Deng, Yebing Yin, Kaili Duan et al.· Frontiers in Plant Science· 0 citations