Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer

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

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Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Авг. 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.

Язык: Английский

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Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

Genes, Год журнала: 2024, Номер 15(1), С. 98 - 98

Опубликована: Янв. 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.

Язык: Английский

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Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

BMC Plant Biology, Год журнала: 2023, Номер 23(1)

Опубликована: Окт. 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.

Язык: Английский

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RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Фев. 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

Язык: Английский

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Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Июль 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.

Язык: Английский

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Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Дек. 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 &lt; 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

Язык: Английский

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The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Март 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

Язык: Английский

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Assembly and analysis of the chloroplast genome of Amorphophallus kachinensis Engler & Gehrmann (Araceae) from Southwestern China: implications for conservation and utilization

Mitochondrial DNA Part B, Год журнала: 2024, Номер 9(4), С. 452 - 456

Опубликована: Апрель 2, 2024

Konjac glucomannan consists of D-mannose and D-glucose units is a hydrocolloid obtained from the corm Amorphophallus species. Due to its bioactive properties, biodegradability, hydrophilic ability, widely used in fields food, medicine, industry. species have been cultivated as cash crops many Asian countries. kachinensis Engler & Gehrmann 1911 naturally distributed southwestern China, Laos, northern Thailand. To help genetic assessment conservation this species, first chloroplast genome A. was sequenced on Illumina sequencing platform. We assembled using software GetOrganelle annotated by Geseq Cpgavas 2. The 173,330 bp long, average GC content 35% (GenBank accession number: PP072244). contained one large single copy, small two inverted repeats, with lengths 92,030 bp, 15,118 33,091 respectively. successfully 132 genes across genome, which consistent other phylogenetic tree indicates sub-divergence genus main groups detected among eight should be treated distinct evolutionarily significant when making strategies. Our study enriched resources could future phylogeographic studies, protection, utilization wild resources.

Язык: Английский

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The complete chloroplast genome assembly of Amorphophallus kiusianus makino 1913 (araceae) from Southern China

Mitochondrial DNA Part B, Год журнала: 2024, Номер 9(4), С. 522 - 526

Опубликована: Апрель 2, 2024

The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms A. populations, we sequenced first chloroplast genome using next-generation sequencing. was 166,269 bp length with an average GC content 36% (GenBank accession number: PP072243). lengths large single-copy (LSC), small (SSC), two inverted repeats (IRs) were 90,701 bp, 14,802 31,383 respectively. One hundred twenty-nine genes annotated genome, including 84 protein-coding genes, 8 rRNA 37 tRNA genes. phylogenetic tree suggested close relationship among kiusianus, yunnanensis, coaetaneus. reported provides valuable genomic resources for future phylogeographic research kiusianus.

Язык: Английский

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