Graph-based mitochondrial genomes of three foundation species in the Saccharum genus DOI Creative Commons
Sicheng Li, Zhen Wang, Jing YanFen

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 4, 2024

Abstract Saccharum belongs to the Andropogoneae and cultivars species in contributes nearly 80% sugar production of world. To explore genomic studies Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) three foundation (Saccharum spontaneum, S. robustum officinarum) using Illumina Oxford Nanopore Technologies sequencing data. The mitogenomes were divided into a total eight types based on contig numbers linkages. All encoded 51 unique genes including 32 protein-coding, 3 ribosomal RNA (rRNA) 16 transfer (tRNA) genes. existence long short repeat-mediated recombinations mitogenome officinarum was revealed confirmed through PCR validation. Furthermore, employing comparative genomics phylogenetic analyses organelle genomes, unveiled evolutionary relationships history major interspecific lineages genus. Phylogenetic homologous fragments between showed that are phylogenetically distinct, they likely parallel rather than domesticated. variations ancient (S. sinense barberi) modern cultivated hybrid) possibly resulted from hybridization involving different accessions. Lastly, this project reported first graph-based species, systematic comparison structural organization, processes, pan-structural variation differential features genomes.

Language: Английский

The mitochondrial genomes of Panax notoginseng reveal recombination mediated by repeats associated with DNA replication DOI
Heyu Yang,

Yang Ni,

Xinyi Zhang

et al.

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 252, P. 126359 - 126359

Published: Aug. 22, 2023

Language: Английский

Citations

26
Assembly and comparative analysis of the complete mitochondrial genome of Echinacanthus longipes (Acanthaceae), endemic to the Sino-Vietnamese karst flora DOI Creative Commons
Chunming Gao, Shu Wang,

Yu‐Song Huang

et al.

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

Published: March 14, 2025

Echinacanthus longipes is an endemic species in the Sino-Vietnamese karst flora family Acanthaceae. It displays distinctive environmental adaptation characteristics regions. Although it provides important model for understanding role of limestone speciation and endemism, mitochondrial genome (mtDNA) E. has not been fully characterized. Here, mtDNA was successfully assembled as a complex structure form two small circular three linear molecules with total length 810,200 bp. The annotated results revealed 36 protein-coding genes (PCGs), 22 tRNA genes, rRNA this mtDNA. Notably, substantial sequence repeats more tRNAs translocations from chloroplast to were identified. Among PCGs longipes, majority 401 RNA editing sites involved amino acid transitions hydrophobic sites. current phylogenetic analysis based on evolution Lamiales close relationship between Avicennia marina. However, comparative analyses, including size, structure, GC contents, reflected variation mitogenomes within Acanthaceae, collinearity confirmed low level conservation genomes related Lamiales. Moreover, Ka/Ks that negative selection occurred most PCGs, notable exception ccmB, which underwent positive selection. Interestingly, ccmB gene had protein This study will be invaluable also extensive information functional genetic adaptive studies regions future.

Language: Английский

Citations

1
The first complete mitochondrial genome assembly and comparative analysis of the fern Blechnaceae family: Blechnopsis orientalis DOI Creative Commons

Yutong Huang,

Yanping Xing, Wenxiao Men

et al.

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

Published: March 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.

Language: Английский

Citations

1
Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome DOI Open Access
Xue Zhang,

Yuanyu Shan,

Jingling Li

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(9), P. 8366 - 8366

Published: May 6, 2023

Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. still lacking, particularly concerning its organelle genome. In this study, was studied to sequence the mitochondrial genome (mitogenome) ascertain assembly, informational content, developmental expression of mitogenome. The findings revealed mitogenome circular measures 515,187 bp in length with GC content 44.05%. It contains 52 unique genes, including 33 protein-coding 19 tRNA three rRNA genes. Additionally, analysis identified 165 SSRs, primarily consisting tetra-nucleotides, 421 pairs dispersed repeats lengths greater than or equal 30, which were mainly forward repeats. Based long reads PCR experiments, we confirmed two long-fragment repetitive elements highly involved recombination process. Furthermore, there 38 homologous fragments detected between chloroplast genome, longest fragment 3962 bp. This first report family Cactaceae. decoding will provide important genetic materials for phylogenetic studies Cactaceae promote utilization germplasm resources.

Language: Английский

Citations

19
Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa DOI
Song Guo, Zeyang Li, Chunlian Li

et al.

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(3)

Published: Feb. 22, 2024

Language: Английский

Citations

8
Unraveling the complex evolutionary features of the Cinnamomum camphora mitochondrial genome DOI
Fuchuan Han, Changwei Bi,

Yunxiao Zhao

et al.

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(7)

Published: June 26, 2024

Language: Английский

Citations

8
Complete mitochondrial genome of Mentha spicata L. reveals multiple chromosomal configurations and RNA editing events DOI
Mei Jiang, Yang Ni,

Jianjie Zhang

et al.

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 251, P. 126257 - 126257

Published: Aug. 11, 2023

Language: Английский

Citations

15
Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae DOI Creative Commons
Yuanyuan Li, Youyan Liu,

Xu Zeng

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: April 23, 2024

Angelica dahurica is a kind of Chinese traditional herbs with economic and ornament value, widely distributed in China. Despite its significance, there have been limited comprehensive investigations on the genome A. , particularly regarding mitochondrial genomes. To investigate conversion between chloroplast genome, complete circular was assembled using Oxford Nanopore Technologies (ONT) long reads. The had length 228,315 base pairs (bp) 45.06% GC content. encodes 56 genes, including 34 protein-coding 19 tRNA genes 3 rRNA genes. Moreover, we discovered that 9 homologous large fragments based sequence similarity. This first report for which could provide an insight communication plastid also give reference medicinal plants within family.

Language: Английский

Citations

6
RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola DOI Creative Commons
Cui Li, Han Liu, Mei Qin

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 6, 2024

Corydalis saxicola , an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, date, the mitochondrial (mt) genome of C. has not been reported, which limits our understanding genetic biological mechanisms . Here, mt was assembled by combining Nanopore Illumina reads. The represented a circular chromosome 587,939 bp length, with overall GC content 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA three rRNA were identified. Codon usage PCGs investigated 167 simple sequence repeats Twelve homologous fragments identified between ct genomes accounting for 1.04% entire genome. Phylogenetic examination 30 taxa provided their evolutionary relationships. We also predicted 779 RNA editing sites C successfully validated 506 (65%) these using PCR amplification Sanger sequencing. In addition, we transcriptionally profiled 24 core roots treated different concentrations CaCl 2 as well organs. These investigations will be useful effective utilization molecular breeding, provide reference further studies genus

Language: Английский

Citations

5
Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl DOI Creative Commons

Yun Song,

Xiaorong Du,

Aoxuan Li

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Nov. 23, 2023

Abstract Background Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear chloroplast genomes of F. have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, genomic DNA yellowish leaf material was extracted, sequenced by using mixture Illumina Novaseq6000 short reads Oxford Nanopore PromethION long reads, sequencing data were assembled annotated. Result The obtained in length 535,692 bp with circular structure, GC content 44.90%. contains 60 genes, including 36 protein-coding 21 tRNA three rRNA genes. We further analyzed RNA editing relative synonymous codon usage, repeats based on data. There 25 homologous sequences between mitochondria genome, which involved transfer 8 9473 genomes. Analysis nucleic acid substitution rate, diversity, collinearity genes revealed that majority may undergone purifying selection, exhibiting slower rate evolution relatively conserved structure. phylogenetic relationships among different species most closely related Olea europaea subsp. Europaea. Conclusion we sequenced, assembled, annotated high-quality genome. results study will enrich , lay foundation for development promote evolutionary analysis Oleaceae species.

Language: Английский

Citations

12