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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Response of Pedunculate Oak (Quercus robur L.) to Adverse Environmental Conditions in Genetic and Dendrochronological Studies

Plants, Год журнала: 2025, Номер 14(1), С. 109 - 109

Опубликована: Янв. 2, 2025

Pedunculate oak (Quercus robur L.) is widely distributed across Europe and serves critical ecological, economic, recreational functions. Investigating its responses to stressors such as drought, extreme temperatures, pests, pathogens provides valuable insights into capacity adapt climate change. Genetic dendrochronological studies offer complementary perspectives on this adaptability. Tree-ring analysis (dendrochronology) reveals how Q. has historically responded environmental stressors, linking growth patterns specific conditions drought or temperature extremes. By examining tree-ring width, density, dynamics, researchers can identify periods of suppression enhancement predict forest future climatic events. further complement by uncovering adaptive genetic diversity inheritance patterns. Identifying markers associated with stress tolerance enables managers prioritize the conservation populations higher potential. These guide reforestation efforts support development climate-resilient populations. integrating data, gain a holistic understanding robur’s mechanisms resilience. This knowledge vital for management sustainable planning in face challenges, ultimately helping ensure long-term viability their ecosystems. The topics covered review are very broad. We tried include most relevant, important, significant studies, but focused mainly relatively recent Eastern European because they species’ area. However, although more than 270 published works have been cited review, we have, course, missed some studies. apologize advance authors those relevant that not cited.

Язык: 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), Год журнала: 2025, Номер unknown

Опубликована: Апрель 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

Язык: Английский

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Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica)

Genomics, Год журнала: 2024, Номер 116(3), С. 110859 - 110859

Опубликована: Май 1, 2024

Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate functions mitochondrial (mt) genome Luffa cylindrica. The mt L. cylindrica contained two chromosomes with lengths 380,879 bp 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA 3 rRNA 1 pseudogene, were identified. About 90.63% codons ended A or U bases, 98.63% monomers A/T, which contributed high A/T content (55.91%) complete genome. Six (ATP8, CCMFC, NAD4, RPL10, RPL5 RPS4) showed positive selection. Phylogenetic analysis indicates that is closely related acutangula. present results provide cylindrica, may facilitate possible variation, evolutionary, molecular breeding studies

Язык: Английский

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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 of Spodiopogon sagittifolius, an endemic and protective species from Yunnan, China

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Март 24, 2025

Spodiopogon sagittifolius, a C4 plant closely related to cultivated crops, is an edible resource and Class II nationally protected species in China. Endemic Yunnan, its populations are declining due habitat destruction, highlighting conservation importance. Despite significance, the molecular phylogenetic relationships genetic mechanisms of adaptive evolution genus remain poorly understood. We successfully assembled annotated first mitochondrial genome S. sagittifolius using HiFi sequencing PMAT tool. The 500,699 bp length with GC content 43.15%. Synteny dN/dS analyses revealed structural functional genomes species, most protein-coding genes under purifying selection (dN/dS < 1). Notably, nad2 exhibited signs positive = 1.49), indicating potential evolution. Extensive RNA editing events were detected across 27 genes, predominantly involving C-to-U conversions, synonymous mutations accounting for 49.65% edits. Strong codon usage bias favoring A/U-ending codons identification repeat sequences suggest enhanced efficiency stress adaptation. Phylogenetic confirmed taxonomic placement within Andropogoneae tribe. This study provides insights into key features linked tolerance These findings establish foundation domestication, implications crop improvement ecological resilience.

Язык: Английский

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Comparative analysis of the complete mitochondrial genomes of Firmiana danxiaensis and F. kwangsiensis (Malvaceae), two endangered Firmiana species in China

Planta, Год журнала: 2025, Номер 261(5)

Опубликована: Апрель 9, 2025

Язык: Английский

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Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria

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

Опубликована: Июнь 1, 2024

Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in cells for energy production, developing an independent genetic system. Therefore, it meaningful to assemble annotate the functions mt genome of plants independently. Though there have been several reports referring Brassica species, B. purpuraria its functional gene variations when compared closely related species has not yet addressed.

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

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Фев. 1, 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 DNA fragments, 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) tended to end at A or U, whereas that low-frequency < G RNA editing sites PCGs were relatively few, only 9 23 cpDNA, respectively. 29 plastid DNAs (MTPTs) derived from three complete trnT-GGU trnH-GUG trnS-GCU Phylogeny collinearity indicated relationship between rotundus closest. rns gene exhibited greatest nucleotide variability, variability infA Chloroplast sequences are more conserved than rRNA sequences. Most organellar been negatively selected highly during evolution. Only six Ka/Ks 1, particular, atp9 atp6 rps7 may undergone potential positive selection. Conclusion validated mtDNA, 15,034 bp reverse complementary sequence. provides valuable genomic resources for identification, evolution, comparative research Cyperaceae.

Язык: Английский

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Assembly and comparative analysis of the multichromosomal mitochondrial genome of globally endangered seagrass Halophila beccarii

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

Опубликована: Ноя. 4, 2024

Halophila beccarii is one of the oldest two generations seagrass plants and 10 species currently at risk extinction worldwide. Therefore, how to effectively protect H. resources from a huge challenge. Molecular biology research can provide scientific basis for conservation. So far, there has been no detailed analysis mitochondrial genome genus Halophila. The was assembled into 28 circular chromosomes, ranging in length 41,738 bp 104,744 bp, with total 1,964,072 GC content 46.71%. It contains 39 genes, including 26 protein coding tRNA 3 rRNA genes. Repeat sequence prediction RNA editing sites revealed 850 dispersed repeats, 1,205 simple 61 tandem 120 sites. Analysis codon usage indicates that codons ending A/U are preferred. Gene migration between chloroplast observed through homologous fragment detection. In addition, Ka/Ks showed most genes experienced negative selection, while only nad3 gene potential positive selection Alismatales. Nucleotide polymorphism variations each gene, rpl10 being significant. comparative shows conserved, but significant differences size structure genomes among different phylogenetic based on reflects exact evolutionary taxonomic status beccarii. this study, we sequenced annotated beccarii, compared it other Our findings enrich mitogenome database highlight help decipher plant history.

Язык: Английский

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