Frontiers in Plant Science, Год журнала: 2024, Номер 15
Опубликована: Ноя. 26, 2024
(Kom.) Kitag., a member of the Apiaceae family, is perennial aromatic herb native to Northeast Asia with applications in culinary and traditional medicine. Despite its significance, most studies on
Язык: Английский
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 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.
Язык: Английский
Процитировано
2
BMC Plant Biology, Год журнала: 2025, Номер 25(1)
Опубликована: Янв. 22, 2025
Abstract Background Red raspberry ( Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast (plastome) have been reported, while there lack of genetic information on its mitogenome. We sequenced assembled the complete mitogenome R. , conducted series investigations comparing it genomes, so as to better gain comprehensive understanding species’ background. Results The represented by one circular chromosome 438,947 bp. Twenty-four core genes, nine variable 26 tRNAs, three rRNAs were annotated. A total 52 SSRs 38 tandem repeat sequences identified. 533 pairs dispersed repeats detected, among which found mediated homologous recombination, resulting in major conformation seven minor conformations. Furthermore, between plastome identified, including six protein-coding genes 12 tRNA genes. also detected 828 fragments mitogenome, trn M-CAU gene. Conclusions In this study, we presented for first time based data obtained from Illumina Oxford Nanopore sequencing platforms. Key characteristics examined, gene composition, repetitive elements, DNA fragments. Additionally, identified multiple recombination events high-quality well-annotated known red will provide essential species classification, evolution analysis, even improvement future.
Язык: Английский
Процитировано
1
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Март 14, 2025
Echinacanthus longipes is an endemic species in the Sino-Vietnamese karst flora family Acanthaceae. It displays distinctive environmental adaptation characteristics regions. Although it provides important model for understanding role of limestone speciation and endemism, mitochondrial genome (mtDNA) E. has not been fully characterized. Here, mtDNA was successfully assembled as a complex structure form two small circular three linear molecules with total length 810,200 bp. The annotated results revealed 36 protein-coding genes (PCGs), 22 tRNA genes, rRNA this mtDNA. Notably, substantial sequence repeats more tRNAs translocations from chloroplast to were identified. Among PCGs longipes, majority 401 RNA editing sites involved amino acid transitions hydrophobic sites. current phylogenetic analysis based on evolution Lamiales close relationship between Avicennia marina. However, comparative analyses, including size, structure, GC contents, reflected variation mitogenomes within Acanthaceae, collinearity confirmed low level conservation genomes related Lamiales. Moreover, Ka/Ks that negative selection occurred most PCGs, notable exception ccmB, which underwent positive selection. Interestingly, ccmB gene had protein This study will be invaluable also extensive information functional genetic adaptive studies regions future.
Язык: Английский
Процитировано
1
Ecology and Evolution, Год журнала: 2025, Номер 15(4)
Опубликована: Март 27, 2025
ABSTRACT Plant mitochondrial genome (mitogenome) has crucial functions underpinning survive, development, and reproduction of organisms. However, the complete mitogenomes have been far less assembled annotated than plastomes even nuclear genomes in plants, due to their highly frequent long repeat sequences genomic structural variations. These further hinder understanding mitogenome evolution restrict potential applications phylogenetic analyses. In this study, we sequenced, assembled, Semiaquilegia guangxiensis explored its usefulness phylogenetics. The results showed that was composed two independent molecules, which had a total length 522,981 bp, GC content 45.69%, 58 genes including 34 protein‐coding (PCGs), 21 tRNA genes, three rRNA genes. A generalized codon usage preference observed among PCGs, 665 RNA editing sites were identified across all base C‐to‐U edits. Moreover, large number repetitive chloroplast‐sourced transferred detected. largest collinear block between S. Paropyrum anemonoides 4282 bp length. analyses based on gene resolved relationships within Ranunculales, close . 19 PCGs ranked according efficiencies resolution several metrics, combined metric suggested mat R, rps 3, nad 5 top loci contributing most phylogeny. As first reported , our findings enrich limited library reecho complex evolutionary dynamics mitogenome, highlight
Язык: Английский
Процитировано
0
Frontiers in Plant Science, Год журнала: 2025, Номер 16
Опубликована: Май 30, 2025
Background Cenchrus fungigraminus is a perennial grass species, which used in the cultivation of edible fungi, helping to resolve land use conflicts between fungus and forest production. It can be also utilized for bioethanol production fiberboard manufacturing. Currently, no report was released on mitochondrial genome. Thus, C. genome assembled annotated utilizing combination Illumina PacBio sequencing data. Results The measures 404,398 bp exhibits linear structure. GC content 43. 98%, 64 characteristic genes were identified, containing 34 protein-coding, six rRNA, 22 tRNA two pseudo-genes, with 17 30 introns. codon usage displayed significant A/T preference. A total 235 dispersed, 93 simple sequence, 38 tandem repeats detected. Furthermore, sequence fragments (17,634 bp) transferred from chloroplast mitochondria, accounting 4.36% complete gene rps2 identified as having highest polymorphism. Additionally, these ( ccmB , nad2 rps7 ) influenced by positive selection. Among reported Poaceae genomes, sizes range 381,065 704,100 bp, ranging 42.27% 44.43%. Three sdh3 rps10 rpl6 are missing genome, indicating rearrangements overall structure low homology. shown that most closely related Saccharum officinarum within family Phylogenetic analysis. interspecific Ka/Ks comparison indicated 28 protein-coding have ratio < 1. Conclusion Therefore, data enriched theoretical basis provided germplasm evaluation new variety utilization.
Язык: Английский
Процитировано
0
Genes, Год журнала: 2024, Номер 15(12), С. 1523 - 1523
Опубликована: Ноя. 27, 2024
Background/Objectives: Chionanthus retusus Lindl. & Paxton is an ornamental tree species native to North China. Research on the mitochondrial genome can elucidate evolution and biological characteristics of C. better protect this important species. Methods Results: This work aimed clarify evolutionary phylogenetic links by sequencing, assembling, annotating, analyzing entire retusus. The single-loop structure that made up had a total length 657,640 bp GC content 44.52%. In total, 37 unique protein-coding genes, 20 tRNA 3 rRNA genes were identified. Numerous repeat sequences migrating fragments chloroplast found. Using construct trees, it was found closest relative rupicola (Lingelsh.) Kiew. Conclusions: research represents first comprehensive set data ancient (>500 yr) specimen. addition elucidating findings contribute Oleaceae database offer valuable insights for future studies in molecular breeding, biology, genetic diversity conservation.
Язык: Английский
Процитировано
0
International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(22), С. 12027 - 12027
Опубликована: Ноя. 8, 2024
Vaccinium bracteatum is a valuable plant used both as food and medicine in China, but low production limits the development of its industry. As such, it important to develop genetic resources for high-value species preservation wild populations utilization. The complete chloroplast nuclear genomes have already been available; however, mitogenome has not yet characterized. Here, V. was assembled using HiFi reads, comparative analysis conducted. circular sequence 708,384 bp with GC content 45.28%, which 67 genes were annotated, including 36 protein-coding genes, 26 tRNA 3 rRNA 2 pseudogenes. Overall, 370 dispersed repeats, 161 simple 42 tandem repeats identified, 360 RNA editing sites predicted. There extensive DNA migration among three genomes. In addition, most underwent purifying selection throughout evolution, nucleotide diversity highly variable. indicated that sizes, structures, gene contents mitogenomes differed significantly, functional relatively conserved Ericales species. Mitogenome-based phylogenetic precise. evolutionary taxonomic status bracteatum. represents last link reference genome lays foundation effective utilization molecular breeding this plant.
Язык: Английский
Процитировано
0
Frontiers in Plant Science, Год журнала: 2024, Номер 15
Опубликована: Ноя. 26, 2024
(Kom.) Kitag., a member of the Apiaceae family, is perennial aromatic herb native to Northeast Asia with applications in culinary and traditional medicine. Despite its significance, most studies on
Язык: Английский
Процитировано
0