Comparative genomics and phylogenetic analysis of mitochondrial genomes of Neocinnamomum

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

Опубликована: Март 6, 2025

Neocinnamomum plants are considered a promising feedstock for biodiesel in China, due to the richness long-chain fatty acids (LCFAs) found their seeds. However, mitochondrial genome (mitogenome) of this genus has not yet been systematically described, and exploration species relationships within using mitogenome sequences is also an uncharted territory. This hindered our understanding diversity evolutionary Neocinnamomum. In study, total 24 individuals representing seven distinct taxa from were subjected Illumina sequencing, N. delavayi was sequenced Oxford Nanopore sequencing technology. We successfully assembled delavayi, which 778,066 bp size exhibits single circular structure. The analysis identified 659 dispersed repeats, 211 simple sequence repeats (SSRs), 30 tandem mitogenome. Additionally, 37 homologous fragments, totaling 9929 bp, between plastid (plastome). codons 41 protein-coding genes (PCGs) had preference ending A/T, codon usage bias majority these influenced by natural selection pressures. Comparative genomic revealed low collinearity significant gene rearrangements species. Phylogenetic resulted classification into six clades, contradicting previous findings based on complete plastomes nuclear ribosomal cistron (nrDNA). PCGs individuals, 86 mutation events identified, included three indels 83 SNPs. Notably, ccmC underwent positive pairwise comparisons pairs. Furthermore, 748 RNA editing sites predicted study enriches knowledge mitogenomes family Lauraceae, provides valuable data foundation evolution research, genetic resource conservation, molecular breeding

Язык: Английский

---

The evolutionary landscape of mitogenomes: Insights from Elsholtzia blanda and comparative analysis of ten related species

Ecological Genetics and Genomics, Год журнала: 2025, Номер 34, С. 100328 - 100328

Опубликована: Янв. 8, 2025

Язык: Английский

---

The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae

Planta, Год журнала: 2025, Номер 261(3)

Опубликована: Фев. 12, 2025

Язык: Английский

---

The Complete Mitochondrial Genome of the Rare Winter-Blooming Rosy Red Cherry Prunus cerasoides

Forests, Год журнала: 2025, Номер 16(3), С. 385 - 385

Опубликована: Фев. 20, 2025

Prunus cerasoides D.-Don is a rare winter-blooming species and distinctive potential germplasm resource for cherry blossoms. We have characterized the mitochondrial genome (mitogenome) of P. acquired monocyclic molecule measuring 421,258 bp. A total 58 unique genes were annotated, comprising 36 protein-coding genes, 19 tRNAs, three rRNAs. In cerasoides, we detected 86 simple sequence repeats, 727 dispersed 21 tandem repeats. 456 RNA editing sites from 34 leading to cytosine uracil transitions. Collinear analysis revealed that mitogenome quite conservative among subgenus Cerasus. Moreover, our study 26 segments plastid genomic DNA had transferred plastome mitogenome. Six found be completely these fragments. The maximum likelihood phylogenetic utilizing mitogenomes 29 distinct Rosaceae supports classification into separate branches. Comprehending characterization crucial elucidating its genetic foundation offers insights evolutionary relationships within species.

Язык: Английский

---

The complete mitochondrial genome and phylogenetic analysis of Lotus corniculatus (Fabaceae, Papilionoideae)

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

Опубликована: Март 11, 2025

Introduction Lotus corniculatus is a perennial leguminous herb and serves as high-quality forage, playing key role in both grassland ecological restoration the development of grazing livestock farming. Methods In this study, we successfully assembled L. mitochondrial genome investigated various related aspects, including genomic features, RNA editing sites, codon preference, gene transfer events, phylogeny. Results discussion We found that length 401,301 bp, its GC content 45.15%. It consists 53 genes, comprising 32 protein-coding 3 ribosomal 18 genes. A total 146 scattered repeats, 8 tandem 124 simple sequence repeats are present genome. thorough examination all genes revealed 485 instances 9579 codons. Additionally, 57 homologous fragments were identified chloroplast genomes, accounting for approximately 4.04% Furthermore, phylogenetic tree based on data from 33 species belonging to four Fabaceae subfamilies two other families validated evolutionary relationship Lotus. These findings have significant implications understanding organization evolution well identification genetic markers. They also offer valuable perspectives relevant devising strategies molecular breeding categorization legumes.

Язык: Английский

---

Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 18, 2025

Lettuce (Lactuca sativa var. ramosa Hort) is an important leaf vegetable that widely cultivates due to its high-quality, short growth cycle, and less diseases. L. Hort belongs Asteraceae family evolutionary relationships with related species of are not completely assessed based on genome sequences. Here, we assembled the whole mitochondrial (mt) Hort, performed a comparative other species. The mt has typical circular structure length 363,324 bp, within GC content accounted for 45.35%. In total 71 genes, comprising 35 protein-coding genes (PCGs), 6 rRNAs, 28 tRNAs, 2 pseudogenes were annotated. Codon preference, RNA-editing sites, repetitive sequences, migrating from chloroplast (cp) genomes investigated in genome. Nucleotide diversity (Pi) showed was relatively conserved. A Bayesian phylogenetic tree closely capitata virosa, which belonged Lactuca genus family. Our findings will provide useful information explore genetic variation, diversity, molecular breeding genus.

Язык: Английский

---

Characterize the Complete Mitogenome of Semiaquilegia guangxiensis and Assess the Efficiency of the Mitochondrial Genes in Ranunculales Phylogeny

Ecology and Evolution, Год журнала: 2025, Номер 15(4)

Опубликована: Март 27, 2025

ABSTRACT Plant mitochondrial genome (mitogenome) has crucial functions underpinning survive, development, and reproduction of organisms. However, the complete mitogenomes have been far less assembled annotated than plastomes even nuclear genomes in plants, due to their highly frequent long repeat sequences genomic structural variations. These further hinder understanding mitogenome evolution restrict potential applications phylogenetic analyses. In this study, we sequenced, assembled, Semiaquilegia guangxiensis explored its usefulness phylogenetics. The results showed that was composed two independent molecules, which had a total length 522,981 bp, GC content 45.69%, 58 genes including 34 protein‐coding (PCGs), 21 tRNA genes, three rRNA genes. A generalized codon usage preference observed among PCGs, 665 RNA editing sites were identified across all base C‐to‐U edits. Moreover, large number repetitive chloroplast‐sourced transferred detected. largest collinear block between S. Paropyrum anemonoides 4282 bp length. analyses based on gene resolved relationships within Ranunculales, close . 19 PCGs ranked according efficiencies resolution several metrics, combined metric suggested mat R, rps 3, nad 5 top loci contributing most phylogeny. As first reported , our findings enrich limited library reecho complex evolutionary dynamics mitogenome, highlight

Язык: Английский

---

Complete analysis and phylogenetic analysis of Polygonatum sibiricum mitochondria

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

Опубликована: Апрель 15, 2025

Abstract In this project, we studied the complete mitogenome of liliaceae medicinal plant Polygonatum sibiricum . The genome is represented by a circular ring molecule with length 691 , 910 bp and GC content 46.33%. Mitochondrial composition slightly biased towards A+T, AT accounting for 53.67%, skewness positive (0.092%). has total sixty-three unique genes, including thirty-nine protein-coding twenty-one transfer RNAs (tRNAs) three ribosomal (rRNAs). We examined codon use, repeat sequence, RNA editing in P. elucidated species classification based on phylogenetic trees twenty-three species. Our results provide comprehensive information show first time evolutionary relationship between Chlorophytum comosum Asparagales family.

Язык: Английский

---

Comprehensive Assembly and Comparative Analysis of Chloroplast Genome and Mitogenome of Prunus salicina var. cordata

Genes, Год журнала: 2025, Номер 16(6), С. 660 - 660

Опубликована: Май 29, 2025

Background: Prunus plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies interspecies identification. Objectives: To clarify the mitochondrial chloroplast genomes of salicina var. cordata, to reveal its evolutionary relationship historical gene flow with domesticated cherries. Methods: In this study, we assembled, annotated, analyzed first P. a species within genus. Results: The genome was found be 484,858 base pairs in length, exhibiting typical circular conformation. Phylogenetic analysis revealed close between domestica salicina, suggesting these two last genomes; phylogeny analysis. Conclusions: provide genomic basis resolving controversies Li-associated plants, elucidating mechanisms, formulating breeding strategies.

Язык: Английский

---

Assembly and comparative analysis of the complete mitogenome of Rubus chingii var. suavissimus, an exceptional berry plant possessing sweet leaves

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

Опубликована: Дек. 23, 2024

Rubus chingii var. suavissimus is a special berry plant of in the Rosaceae family. Its leaves contain high-sweetness, low-calorie, and non-toxic sweet ingredients, known as rubusoside. As medicine food biofunctional plant, it combination “tea, sugar, medicine.” In this study, complete mitogenome R. was successfully assembled annotated based on PacBio HiFi sequencing technology. The typical master circle structure, spanning 432,483 bp containing 34 unique protein-coding genes (PCGs), 20 tRNAs, 3 rRNAs. majority these PCGs subjected to purifying selection, only one gene ( ccmB ) showed sign positive selection. contained large number repeats, homogeneous fragments transferring between plastid genome mitogenome, with total 55 pairs mitochondrial sequences (MTPTs), size 56,913 bp. Comparative analysis that non-coding region had undergone frequent rearrangements during evolution, but coding still highly conserved. Furthermore, maximum likelihood Bayesian inference phylogenetic trees were reconstructed 10 shared 36 species. topological structures two consistent APG IV classification system high support rates. general, study clarifies provides valuable insights into genetic evolution

Язык: Английский

---