Assembly and analysis of the complete mitochondrial genome of Prunus davidiana (Rosaceae)

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Март 27, 2025

Prunus davidiana is an excellent woody species with high resistance to various abiotic and biotic stresses. The also a potential gene donor due its important developmental prospects. However, the characterisation of mitochondrial genome (mitogenome) remains unexplored. In this study, we sequenced assembled mitogenome P. using reads from Illumina sequencing Oxford Nanopore platform. According results, 407,608 bp in length, GC content 45.5%. It contains 64 genes, including 39 protein-coding 22 tRNA genes 3 rRNA genes. Codon usage, repetitive sequences, nonsynonymous synonymous substitution ratios, RNA editing, synteny, phylogenetic relationships among Rosaceae migration events were investigated. addition, two novel indel markers developed distinguish several (i.e. pseudocerasus , armeniaca salicina ). results our analyses provide valuable information theoretical basis for future research on .

Язык: Английский

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The first complete mitochondrial genome assembly and comparative analysis of the fern Blechnaceae family: Blechnopsis orientalis

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Март 20, 2025

Introduction Blechnopsis orientalis (L.) C. Presl is a medicinal and edible fern species belonging to the Blechnaceae family. Currently, complete mitochondrial genome of B. , as well those other species, remains unreported, studies on are limited. Methods In this study, was sequenced using both Nanopore PromethION Illumina NovaSeq 6000 platforms. Genome annotation performed MITOFY MFANNOT, with structural visualization via OGDRAW. In-depth analyses were conducted, including assessments non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, repeat sequence identification, RNA editing site prediction, collinearity, identification homologous fragments between chloroplast genomes. Finally, we employed maximum likelihood (ML) Bayesian (BI) methods analyze phylogenetic relationships among nine lycophyte species. Results The has complex structure comprising 80 contigs, total length 501,663 bp GC content 48.53%. A 179 genes identified, 40 protein-coding (PCGs), 98 tRNA genes, rRNA one pseudogene ( rps11 ). Phylogenetic analysis based PCGs from aligned described in Pteridophyte Phylogeny Group I (PPG I) system. Further comparison ten reported revealed that these plants highly conserved, despite significant rearrangements genome. Discussion findings study provide valuable insights into evolutionary contribute understanding characteristics ferns lycophytes.

Язык: Английский

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De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Март 24, 2025

Prunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible ornamental value. However, the mitochondrial genomes (mitogenomes) of species remain largely unexplored. Here, we successfully assembled mitogenomes five ( P. campanulata , fruticosa mahaleb pseudocerasus sp eciosa ), revealing common circular structures. The exhibited sizes ranging from 383,398 bp to 447,498 bp, with GC content varying between 45.54% 45.76%. A total 62 69 genes were annotated, variability in copy number protein-coding (PCGs) tRNA genes. Mitogenome collinearity analysis indicated genomic rearrangements across species, driven by repetitive sequences, particularly dispersed repeats. Additionally, displayed highly conserved codon usage RNA editing patterns, highlighting evolutionary conservation PCGs. Phylogenetic analyses confirmed monophyly subg. although notable phylogenetic incongruences observed plastid datasets. These results provide resources for forthcoming studies on evolution molecular breeding mitogenomes, enhancing overall comprehension mitogenome structure within .

Язык: Английский

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Assembly and comparative analysis of the complete mitochondrial genome of <i>Yulania liliiflora</i>: an ornamental plant with high medicinal value

Ornamental Plant Research, Год журнала: 2025, Номер 5(1), С. 0 - 0

Опубликована: Янв. 1, 2025

Язык: Английский

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De novo assembly and comparative analysis of the first complete mitogenome in Distylium (Distylium racemosum)

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Май 15, 2025

The genus Distylium (Hamamelidaceae) is highly valued for its applications in ornamental horticulture, industry, and construction. Although plastid genomes (plastomes) of multiple species have been characterized, no mitochondrial (mitogenomes) reported this genus. In study, we assembled annotated the complete mitogenome racemosum using HiFi sequencing data. comprises a longer circular chromosome shorter linear (904,264 bp total length), revealing structurally complex conformation. We 67 genes, including 43 protein-coding genes (PCGs), 21 tRNA three rRNA genes. Analyses identified exceptionally high repetitive sequence content, with 304 simple repeats, 1,508 dispersed 50 tandem representing highest repeat content among Saxifragales mitogenomes to date. Additionally, 49 DNA sequences were detected, only one plastid-derived gene ( trnC-GCA ) transferred mitogenome. predicted 697 RNA editing sites across 42 PCGs, further underscoring genome’s dynamic evolution. Phylogenetic reconstruction based on plastomes from 18 indicated D. occupied basal position within Saxifragales, which consistent APG IV classification system. This study provides first comprehensive mitogenomic resource genus, offering valuable insights molecular classification, identification, germplasm conservation plants.

Язык: Английский

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

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

Опубликована: Май 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.

Язык: Английский

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Unraveling the mitochondrial genome of the medicinal Chinese motherwort (Leonurus japonicus, Lamiaceae): structural dynamics, organelle-to-nuclear gene transfer, and evolutionary implications

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Июнь 3, 2025

Introduction Leonurus japonicus (Chinese motherwort) is a medicinal Lamiaceae species renowned for its pharmacological compounds, yet mitochondrial genome remains unexplored. Elucidating mitogenomic structure and evolution can inform plant genetics, phylogenetics, molecular breeding. Methods We assembled the complete of L. using combination Oxford Nanopore long reads Illumina short reads. Three assembly strategies— de novo with PMAT Flye, hybrid Unicycler—were integrated validated via read mapping comparison to reference mitogenomes ( Salvia miltiorrhiza, Arabidopsis thaliana, Liriodendron tulipifera ). Annotation employed GeSeq, tRNAscan-SE, manual curation. Repeat elements (SSR, tandem, dispersed) were identified MISA, TRF, REPuter; plastid‐to‐mitochondrion transfers (MTPTs) detected by BLASTN against plastome; RNA editing sites predicted Deepred-mt. Phylogenetic synteny analyses conducted IQ-TREE, MAFFT alignments 24 conserved PCGs, NGenomeSyn visualization. Results The circular mitogenome spanned 384,199 bp (45.1% GC) encoded 35 protein-coding genes, 11 tRNAs, 3 rRNAs. 241 SSRs, 13 tandem repeats, 90 dispersed indicating extensive recombination potential. Thirty-one MTPTs totaling 24,818 (6.46% mitogenome) identified. Comparative revealed strong purifying selection (Ka/Ks &lt; 1) across most selective signatures in atp4 ccmB. inference placed among Lamiales, closely allied Scutellaria tsinyunensis Rotheca serrata . Synteny maps demonstrated frequent rearrangements. Deepred-mt 408 C-to-U sites, notably nad4 ccmB , including novel start stop codons. Discussion exhibits marked structural plasticity, reflecting dynamic repeats organelle‐to‐organelle DNA transfers. Extensive underscores post-transcriptional regulation function. These findings enrich genomic resources support phylogenetic evolutionary studies Lamiaceae, lay groundwork breeding conservation strategies targeting traits.

Язык: Английский

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Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 204, С. 108253 - 108253

Опубликована: Ноя. 29, 2024

Язык: Английский

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