Mitochondrial DNA Part B, Journal Year: 2024, Volume and Issue: 9(7), P. 865 - 870
Published: July 2, 2024
(Dennst.) Nicolson, 1885, often known as elephant foot yam, is a tropical tuber crop that originates from south-east Asia and belongs to the Araceae family. It for its high production potential popularity medicinal plant. However, phylogeny genes this species are still unavailable. In study, first complete chloroplast genome of
Language: Английский
BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)
Published: Aug. 8, 2024
Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. from extinction poses a significant challenge. A profound understanding genetic foundation crucial. To date, research on complete mitochondrial genome not yet been reported.
Language: Английский
Citations
7
Genes, Journal Year: 2024, Volume and Issue: 15(1), P. 98 - 98
Published: Jan. 15, 2024
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. through a de novo assembly strategy. We carried out comparative genomic analyses found that, comparison plastid (plastome) showing high degree structural conservation, structure relatively complex, intricate ring 16 connections, owing to five repetitive sequences. The was 783,161 bp GC content 44.8% contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA 3 rRNA genes. counted 579 RNA editing events CDS 12,828 codons all CDSs mitogenome. Furthermore, 24 unique sequence transfer fragments were between plastome, 8 plastome corresponding 2.39% Mitogenomes had shorter but more collinear regions, evidenced by organelles non-parasitic chingii, hemiparasitic Pedicularis chinensis, holoparasitic Aeginetia indica Orobanchaceae family. Moreover, from species, size mitogenomes species did decrease gradually. Instead, smallest P. 225,612 bp. findings fill gap research promote progress organelle family, provide clues for molecular breeding.
Language: Английский
Citations
6
Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15
Published: Feb. 6, 2024
Corydalis saxicola , an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, date, the mitochondrial (mt) genome of C. has not been reported, which limits our understanding genetic biological mechanisms . Here, mt was assembled by combining Nanopore Illumina reads. The represented a circular chromosome 587,939 bp length, with overall GC content 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA three rRNA were identified. Codon usage PCGs investigated 167 simple sequence repeats Twelve homologous fragments identified between ct genomes accounting for 1.04% entire genome. Phylogenetic examination 30 taxa provided their evolutionary relationships. We also predicted 779 RNA editing sites C successfully validated 506 (65%) these using PCR amplification Sanger sequencing. In addition, we transcriptionally profiled 24 core roots treated different concentrations CaCl 2 as well organs. These investigations will be useful effective utilization molecular breeding, provide reference further studies genus
Language: Английский
Citations
5
BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)
Published: July 3, 2024
Abstract Background Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic ecological value. To elucidate the structural characteristics, variation, evolution of organelle genome C. , we sequenced, assembled, compared its mitochondrial chloroplast genomes. Results We assembled genomes . The total length (mtDNA) was 927,413 bp, with a GC content 40.59%. It consists two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, five rRNAs. (cpDNA) 186,204 containing 93 PCGs, 40 8 mtDNA cpDNA contained 81 129 tandem repeats, respectively, 346 1,170 dispersed both which have 270 simple sequence repeats. third high-frequency codon (RSCU > 1) organellar tended to end at A or U, whereas low-frequency < G RNA editing sites PCGs were relatively few, only 9 23 cpDNA, respectively. 28 plastid DNAs (MTPTs) derived from three complete trnT-GGU trnH-GUG trnS-GCU Phylogeny collinearity indicated that relationship between rotundus are closest. rns gene exhibited greatest nucleotide variability, variability infA Most negatively selected highly evolutionarily conserved. Only six Ka/Ks 1; particular, atp9 atp6 rps7 may undergone potential positive selection. Conclusion validated contains 15,034 bp reverse complementary sequence. provides valuable genomic resources for identification, evolution, comparative research Cyperaceae.
Language: Английский
Citations
5
BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)
Published: Oct. 25, 2023
Abstract Background Punica granatum is a fundamentally important fruit tree that has economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study P. mitogenome was sequenced assembled to further understanding organization, variation, evolution mitogenomes species. Results The structure multi-chromosomes with seven circular contigs, measuring 382,774 bp length 45.91% GC content. It contained 74 genes, including 46 protein-coding 25 tRNA three rRNA genes. There were 188 pairs dispersed repeats lengths 30 or greater, primarily consisting reverse complementary repeats. analysis identified 114SSRs 466 RNA editing sites. Analyses codon usage, nucleotide diversity gene migration from chloroplast also conducted. collinear comparative structures between its proximal species indicated ‘Taishanhong’ closely related ‘Qingpitian’ Lagerstroemia indica. Phylogenetic examination based confirmed evolutionary relationship. Conclusion results offered crucial information biology pomegranate highlighted ways promote utilization species’ germplasm.
Language: Английский
Citations
13
Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15
Published: March 6, 2024
, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy ancient China. In this study, we assembled annotated the complete mitochondrial genome (mitogenome) of
Language: Английский
Citations
4
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: Dec. 8, 2023
Introduction Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, genetic background investigations of P. . However, the mitochondrial this species has not systematically described, owing complexity plant mitogenome. Methods In present research, complete was assembled, annotated, characterized. The genomic features, content repetitive sequences were analyzed. variation phylogenetic analysis have extensively enumerated. Results discussion mitogenome circular molecule total length 405,855 bp GC 45.63%, which are smallest size highest among known genomes. encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), ribosomal RNA 19 transfer genes. rich sequences, counting 112 simple sequence repeats, 15 tandem 50 interspersed repeat 11,793 bp, accounting for 2.91% genome. Leucine (Leu) predominant amino acid PCGs, frequency 10.67%, whereas cysteine (Cys) tryptophan (Trp) least adopted. most frequently used codon UUU (Phe), relative synonymous usage (RSCU) value 1.12. Selective pressure calculated based on 20 shared PCGs mitogenomes 32 species, subjected purifying selection (Ka/Ks < 1), ccmC ccmFn underwent positive selection. A 262 potential editing sites 26 identified. Furthermore, 56 chloroplast-derived fragments ascertained mitogenome, ranging from 30 858 mainly located across IGS (intergenic spacer) regions or rRNA These findings verify occurrence intracellular events chloroplast mitochondria. relationship supported by data other taxa Rosaceae family. Understanding characteristics great importance promote comprehension its study provides basis breeding
Language: Английский
Citations
10
BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)
Published: Jan. 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.
Language: Английский
Citations
0
Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)
Published: March 18, 2025
Lettuce (Lactuca sativa var. ramosa Hort) is an important leaf vegetable that widely cultivates due to its high-quality, short growth cycle, and less diseases. L. Hort belongs Asteraceae family evolutionary relationships with related species of are not completely assessed based on genome sequences. Here, we assembled the whole mitochondrial (mt) Hort, performed a comparative other species. The mt has typical circular structure length 363,324 bp, within GC content accounted for 45.35%. In total 71 genes, comprising 35 protein-coding genes (PCGs), 6 rRNAs, 28 tRNAs, 2 pseudogenes were annotated. Codon preference, RNA-editing sites, repetitive sequences, migrating from chloroplast (cp) genomes investigated in genome. Nucleotide diversity (Pi) showed was relatively conserved. A Bayesian phylogenetic tree closely capitata virosa, which belonged Lactuca genus family. Our findings will provide useful information explore genetic variation, diversity, molecular breeding genus.
Language: Английский
Citations
0
BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)
Published: March 31, 2025
The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on mitochondrial genome (mitogenome) hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized complete mitogenome genus Cymbaria L. sensu stricto (C. mongolica C. daurica). A total 51 unique genes, including 33 protein-coding three rRNA 15 tRNA shared by mitogenomes two plants, exhibiting gene content characteristic autotrophic daurica a pentacyclic chromosome structure (their major conformation), with lengths 1,576,465 bp 1,539,836 bp, respectively. Moreover, identified validated presence four minor conformations mediated pairs large repeats (> 1000 in size) eight six daurica. We further explored codon usage, RNA editing sites, selective pressure, nucleotide diversity mitogenomes. Phylogenetic analyses 26 species Lamiales revealed that form sister clade to other lineages Orobanchaceae. Extensive mitogenomic rearrangements also observed between five closely related species. Although plastid sequences mitogenomes, (MTPTs) their represent only 2.37% 1.74%, Additionally, there minimal evidence intracellular horizontal transfer, few genes (rpl22, rps3, ycf2) showing low bootstrap support (BS ≤ 70%) relationships potential host plants Allium mongolicum, Leymus chinensis, Saposhnikovia divaricata, reported first time, which multiple repeat-mediated recombination little no transfer. Our findings provide valuable genetic insights studies evolution
Language: Английский
Citations
0