De novo assembly of the mitochondrial genome of Glycyrrhiza glabra and identification of two types of homologous recombination configurations caused by repeat sequences

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 6, 2025

Glycyrrhiza glabra, which is widely used in medicine and therapy, known as the 'king of traditional Chinese medicine'. In this study, we successfully assembled annotated mitochondrial chloroplast genomes G. glabra via high-throughput sequencing technology, combining advantages short-read (Illumina) long-read (Oxford Nanopore) sequencing. We revealed ring structure genome, spans 421,293 bp with 45.1% GC content 56 genes. Notably, identified 514 repetitive sequences, including 123 Simple sequence repeats (SRs), 3 Tndem (TSRs), 388 Dispersed (DSRs). 79 out DSRs potentially involved homologous recombination. five forward four palindromic that facilitate recombination induce alterations genome structure. corroborated finding polymerase chain reaction (PCR). Furthermore, chloroplast-derived fragments within offering novel insights into evolutionary history plant genomes. predicted 460 potential RNA editing sites, primarily involving cytosine-to-uracil transitions. This study reveals complexity sequence-mediated provides new its structure, function, evolution. These findings have important implications for conservation biology, population genetics, studies, underscoring role sequences dynamics highlighting need further research on evolution function plants.

Language: Английский

---

Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 20, 2025

Introduction Garuga forrestii W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This plays crucial role maintaining biodiversity these ecosystems. Methods We performed de novo assembly mitochondrial genome using PMAT (v.1.5.4), resulting typical circular molecule 606,853 bp. The consists 31 tRNA genes, 3 rRNA 35 protein-coding and 1 pseudogene. study also investigates RNA editing sites evolutionary patterns. Results exhibits low proportion repetitive sequences (3.30%), suggesting highly conserved structure. A high copy number trnM-CAT gene (4 copies) noted, which may contribute genomic rearrangement adaptive evolution. Among 476 sites, hydrophilic-hydrophobic hydrophobic-hydrophobic events are most common, accounting for 77.10%. Negative selection predominates among genes (Ka/Ks < 1), while few (e.g., matR , nad3 rps1 rps12 rps4 ) show signs positive > potentially conferring advantages. Additionally, significant A/T bias observed at third codon position. Phylogenomic analysis supports APG IV classification, with no evidence horizontal transfer. Discussion offers valuable insights into mechanisms processes . It enhances our understanding species' biogeography tropical Southeast Asia Southwest providing key information on history this genus.

Language: Английский

---

Assembly of the Hippophae salicifolia Mitochondrial Genome and Insights into Adaptation to Extreme Environments

Biology, Journal Year: 2025, Volume and Issue: 14(4), P. 448 - 448

Published: April 20, 2025

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to Himalayas. The 475,105 bp has a 44.80% GC content overall AT bias, comprising 74 genes (37 protein-coding, 31 tRNA, three rRNA, pseudogenes). We identified extensive repetitive elements, including 188 SSRs, 20 tandem repeats, 455 dispersed explored their potential roles in evolution. Codon usage analysis showed bias for codons ending A or U, while RNA editing revealed 415 sites that mostly convert hydrophilic hydrophobic amino acids. Phylogenetic collinearity analyses clarified evolutionary relationships within uncovered rearrangements. In addition, gene transfer was detected between chloroplast genomes. Ka/Ks nucleotide diversity indicate most are under purifying selection, with some possibly undergoing positive selection. Overall, these findings enhance our understanding structural features H. salicifolia provide valuable insights genetic improvement conservation species.

Language: Английский

---

Structural Features and Synteny Analysis of the Sea Buckthorn Mitochondrial Genome

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 23, 2025

Background Sea buckthorn (Hippophae rhamnoides L.) is a plant of significant economic, culinary, medicinal, ecological, and societal value. In order to gain deeper understanding the sea mitochondrial genome, sequencing assembly genome was performed, its substructures were explored in this study. Results The seabuckthorn consists two circular chromosomes, with lengths 297,507 bp 167,037 bp, respectively. It encompasses 36 annotated protein-coding genes, 3 rRNA 25 tRNA genes. addition, 212 pairs repeats detected, including pair that mediated homologous recombination chromosomes form conformations. existence these conformations confirmed through PCR amplification Sanger sequencing. A total 162 SSR loci identified genome. There are 30 fragments chloroplast genomes, length 44,950 accounting for 9.89% genomes. Conclusions summary, study conducted annotation providing comprehensive plant. This knowledge great significance effective utilization genetic improvement seabuckthorn, especially breeding evolutionary analysis cytoplasmic male sterility.

Language: Английский

---

Assembly and comparative analysis of the complete mitogenome of Rubus chingii var. suavissimus, an exceptional berry plant possessing sweet leaves

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 23, 2024

Rubus chingii var. suavissimus is a special berry plant of in the Rosaceae family. Its leaves contain high-sweetness, low-calorie, and non-toxic sweet ingredients, known as rubusoside. As medicine food biofunctional plant, it combination “tea, sugar, medicine.” In this study, complete mitogenome R. was successfully assembled annotated based on PacBio HiFi sequencing technology. The typical master circle structure, spanning 432,483 bp containing 34 unique protein-coding genes (PCGs), 20 tRNAs, 3 rRNAs. majority these PCGs subjected to purifying selection, only one gene ( ccmB ) showed sign positive selection. contained large number repeats, homogeneous fragments transferring between plastid genome mitogenome, with total 55 pairs mitochondrial sequences (MTPTs), size 56,913 bp. Comparative analysis that non-coding region had undergone frequent rearrangements during evolution, but coding still highly conserved. Furthermore, maximum likelihood Bayesian inference phylogenetic trees were reconstructed 10 shared 36 species. topological structures two consistent APG IV classification system high support rates. general, study clarifies provides valuable insights into genetic evolution

Language: Английский

---