Assembly and analysis of the first complete mitochondrial genome sequencing of main Tea-oil Camellia cultivars Camellia drupifera (Theaceae): revealed a multi-branch mitochondrial conformation for Camellia

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 3, 2025

Language: Английский

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De novo assembly of the complete mitochondrial genomes of two Camellia-oil tree species reveals their multibranch conformation and evolutionary relationships

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 23, 2025

Language: Английский

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Methods for assembling complex mitochondrial genomes in land plants

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5169 - 5174

Published: Feb. 1, 2024

The large size and complex structural rearrangements inherent in the mitochondrial genomes of land plants pose challenges for their sequencing. Originally, assembly these required cloning DNA fragments followed by Sanger Subsequently, advent next-generation sequencing significantly expedited process. This review highlights examples plant genome employing various technologies, including 454 sequencing, Illumina short reads, Pacific Biosciences or Oxford Nanopore Technology long reads. combination reads hybrid has proven to be most efficient approach achieving reliable assemblies genomes.

Language: Английский

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Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea

Journal of Molecular Evolution, Journal Year: 2023, Volume and Issue: 91(2), P. 156 - 168

Published: March 1, 2023

Language: Английский

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Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 25, 2024

Abstract Background Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin evolutionary history. Result We sequenced complete organelle genomes gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited quadripartite structure large single-copy region (LSC), small (SSC), pair inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, four rRNAs. mitochondrial (681,203 alternative conformations alongside monocyclic structure: 61 encoding 38 20 three rRNAs, RNA editing-impacting genes, ATP6 , RPL16 COX2 NAD4L NAD5 NAD7 RPS1 . Comparative analyses revealed frequent recombination events apparent rRNA gene gains losses Theaceae. In genomes, protein-coding strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic confirmed Stewartieae's early divergence within shedding light on characteristics evolution Conclusions studied detailed characterization structure, composition, repeated sequences, along with identification lateral transfer (LGT) complexities. discovery number repetitive sequences simple repeats (SSRs) has led new molecular phylogenetic markers. Decoding organellar provides valuable genomic resources for further studies plant phylogenomics biology.

Language: Английский

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

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

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Assembly and analysis of the complete mitochondrial genome of an endemic Camellia species of China, Camellia tachangensis

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

Published: April 1, 2025

Background Camellia tachangensis F. C. Zhang is an endemic Camellia species of the junction Yunnan, Guizhou and Guangxi Provinces in China. It characterized by a primitive five-chambered ovary morphology serves as botanical source renowned “Pu’an Red Tea”. Unfortunately, populations have declined due to destruction their habitats human activities. The lack mitochondrial genomic resources has hindered research into molecular breeding phylogenetic evolution C. tachangensis. Result In this study, we had sequenced, assembled, annotated genome reveal its genetic characteristics relation with other species. assembly result indicated that sequence was 746,931 bp (GC content = 45.86%). consisted one multibranched (Chr1) circular (Chr2), Chr1 capable producing 7 substructures. comparative analysis chloroplast DNA revealed 23 pairs homologous fragments, 10 fully preserved tRNA genes within them. Comparison interspecies Ka/Ks mutations protein-coding (PCGs) were predominantly shaped purifying selection throughout (Ka/Ks < 1). tree constructed from CDS certain variants sinensis distinct species, forming clade relatively low support (BS 22%, PP 0.41). Meanwhile, genomes-based analyses most closely related taliensis, makuanica, gymnogyna, strong statistical 100, 1.00). Conclusions Our study deciphered structure tachangensis. These findings not only enhanced our comprehension complexity diversity structures but also established foundational data framework for future on programs relationship involving

Language: Английский

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Analysis of the complete mitogenomes of three high economic value tea plants (Tea-oil Camellia) provide insights into evolution and phylogeny relationship

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: April 24, 2025

Tea-oil Camellia species play a crucial economic and ecological role worldwide, yet their mitochondrial genomes remain largely unexplored. In this study, we assembled analyzed the complete of oleifera C. meiocarpa, revealing multi-branch structures that deviate from typical circular genome observed in most plants. The mitogenomes span 953,690 bp (C. oleifera) 923,117 meiocarpa), containing 74 76 annotated genes, respectively. Comparative genomic analyses indicated meiocarpa share closer genetic relationship, whereas drupifera is more distantly related. Codon usage analysis revealed natural selection plays dominant shaping codon bias these genomes. Additionally, extensive gene transfer events were detected among three species, highlighting dynamic nature evolution Camellia. Phylogenetic reconstruction based on genes exhibited incongruence with chloroplast phylogenies, suggesting potential discordance due to hybridization events, incomplete lineage sorting (ILS), or horizontal (HGT). Furthermore, identified species-specific markers, which provide valuable molecular tools for distinguishing species. Our findings enhance understanding diversity Camellia, offering essential resources phylogenetics, identification, evolutionary research woody

Language: Английский

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Assembly and analysis of the complete mitochondrial genome of an endemic Camellia species of China, Camellia tachangensis

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

Published: May 15, 2025

Camellia tachangensis F. C. Zhang is an endemic species of the junction Yunnan, Guizhou and Guangxi Provinces in China. It characterized by a primitive five-chambered ovary morphology serves as botanical source renowned "Pu'an Red Tea". Unfortunately, populations have declined due to destruction their habitats human activities. The lack mitochondrial genomic resources has hindered research into molecular breeding phylogenetic evolution tachangensis. In this study, we had sequenced, assembled, annotated genome reveal its genetic characteristics relation with other species. assembly result indicated that sequence was 746,931 bp (GC content = 45.86%). consisted one multibranched (Chr1) circular (Chr2), Chr1 capable producing 7 substructures. comparative analysis chloroplast DNA revealed 23 pairs homologous fragments, 10 fully preserved tRNA genes within them. Interspecies comparison Ka/Ks ratios mutations protein-coding (PCGs) were predominantly shaped purifying selection throughout (Ka/Ks < 1). CDS-based tree lineage, phylogenetically independent sections Oleifera, Camellia, Heterogenea, Chrysantha. However, it also did not support clustering certain variants sinensis, extremely low (BS 22, PP 0.41). Meanwhile, PCG-based formed strongly supported basal clade 100, 1.00), alongside makuanica (NC_087766), taliensis (NC_022264), gymnogyna (NC_039626). Our study deciphered structure These findings only enhanced our comprehension complexity diversity structures species, but established foundational data framework for future on programs relationship involving related

Language: Английский

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Assembly and characterization analysis of the complete mitochondrial genome of Lithocarpus litseifolius (Hance) Chun

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: April 20, 2024

Language: Английский

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