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, 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

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

Genomics, Journal Year: 2024, Volume and Issue: 116(3), P. 110859 - 110859

Published: May 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

Language: Английский

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

Plants, Journal Year: 2025, Volume and Issue: 14(1), P. 109 - 109

Published: Jan. 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.

Language: 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, 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

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

Published: March 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.

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

Planta, Journal Year: 2025, Volume and Issue: 261(5)

Published: April 9, 2025

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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De-novo assembly and comparative analysis of the complete mitogenome of traditional Chinese medicine Strobilanthes sarcorrhiza

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

Published: May 21, 2025

Abstract Background Strobilanthes sarcorrhiza is a traditional medicinal plant known for its heat-clearing and kidney-nourishing properties. While plastid genome has been reported, there scarcity of genetic information regarding mitogenome, leading to unclear phylogenetic relationships. We sequenced assembled the complete mitogenome conducted series analyses in conjunction with gain better understanding species’ background. Results The comprised linear structure spanning 617,134 bp. It included 35 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), 3 ribosomal (rRNAs) that have annotated. Additionally, 122 simple sequence repeats (SSRs) 25 tandem were identified. A total 1,482 pairs dispersed detected, which account 17.58% entire mitogenome. Furthermore, 37 migration fragments between mitochondrial genomes discovered, consisting 5 PCGs, 7 tRNAs, 1 rRNA. Based on analysis 38 mitogenomes 46 genomes, evolutionary relationship position S. elucidated. Conclusions This study has, first time, provided insights into genomic characteristics clarified position. These findings offered significant future identification classification this genus, as well breeding plants.

Language: Английский

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

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

Published: June 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.

Language: Английский

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