Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement DOI Creative Commons
Xiangyan He, Jinming Chen, Zhizhong Li

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(9)

Published: Aug. 31, 2024

Abstract Scheuchzeria palustris , the only species in Scheuchzeriaceae family, plays a crucial role methane production and transportation, influencing global carbon cycle maintaining ecosystem stability. However, it is now threatened by human activities warming. In this study, we generated new organelle genomes for S. with plastome (pt) measuring 158,573 bp mitogenome (mt) 420,724 bp. We predicted 296 RNA editing sites mt protein‐coding genes (PCGs) 142 pt‐PCGs. Notably, abundant pt‐PCGs likely originated from horizontal gene transfer between mitogenome. Additionally, identified positive selection signals four mt‐PCGs ( atp4 ccmB nad3 sdh4 ) one pt‐PCG rps7 ), which may contribute to adaptation of low‐temperature high‐altitude environments. Furthermore, 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed dispersed repeats near most MTPT. Phylogenetic trees reconstructed mt‐ showed topologies consistent APG IV system. conflicting position can be explained significant differences substitution rates its p < .001). conclusion, our study provides vital genomic resources support future conservation efforts explores mechanisms .

Language: Английский

The Complete Mitochondrial Genome of the Rare Winter-Blooming Rosy Red Cherry Prunus cerasoides DOI Open Access
Yujun Wang,

Mingjun He,

Feifei Han

et al.

Forests, Journal Year: 2025, Volume and Issue: 16(3), P. 385 - 385

Published: Feb. 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.

Language: Английский

Citations

0
Global advances in phylogeny, taxonomy and biogeography of Lauraceae DOI Creative Commons
Lang Li, Bing Liu, Yu Song

et al.

Plant Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Assembly and comparative analysis of the complete mitochondrial genome of <i>Yulania liliiflora</i>: an ornamental plant with high medicinal value DOI Creative Commons
Yunhan Chen, Wei Liu, Jing Qiu

et al.

Ornamental Plant Research, Journal Year: 2025, Volume and Issue: 5(1), P. 0 - 0

Published: Jan. 1, 2025

Language: Английский

Citations

0
Comparative analysis of the organelle genomes of seven Rosa species (Rosaceae): insights into structural variation and phylogenetic position DOI Creative Commons
Rongxiang Zhang, Shuwen Liu, Ying Liu

et al.

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

Published: May 8, 2025

The genus Rosa belongs to the family Rosaceae within order Rosales, which is one of more ancient plant lineages. At present, complete mitochondrial genome spp. still rarely reported, and studies on are limited. In this study, R. laevigata was sequenced using both Pacbio Sequel II DNB-SEQ-T7 platforms. second- third-generation data for other five species were downloaded from NCBI database. Genome annotation performed Geneious, with structural visualization via CPGview. In-depth analyses conducted, including assessments non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, collinearity, identification homologous fragments between chloroplast genomes. Finally, we employed maximum likelihood (ML) methods analyze phylogenetic relationships among species. sizes ranged 156,342 bp (R. laevigata) 157,214 agrestis). GC content varied 37.2% 37.3%, number genes 129 131. genomes all circular, lengths 271,191 338,975 bp, containing 52 59 genes. Codon analysis indicated a preference A/T-ending codons in Four highly differentiated regions (rps19, ndhF, ycf1, psbM-trnD-GUC) plastomes 7 identified, can serve as molecular markers future genetic diversity. Compared PCGs plastome, displayed higher non-synonymous synonymous ratio. We also observed extensive gene transfer mitochondria chloroplasts, particularly rrn16 rpl23 genes, commonly found These events likely occurred ancestor around 4.46 Mya. Estimates divergence indicate that rapid differentiation took place Mya, potentially influenced by uplift Qinghai-Tibet Plateau during Late Miocene. This study enriches resources lays groundwork development markers, analyses, research into evolution organelle

Language: Английский

Citations

0
De novo assembly and comparative analysis of the first complete mitogenome in Distylium (Distylium racemosum) DOI Creative Commons

Yaling Wang,

Zhongxiao Zhang,

Xinru Chen

et al.

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

Published: May 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.

Language: Английский

Citations

0
De-novo assembly and comparative analysis of the complete mitogenome of traditional Chinese medicine Strobilanthes sarcorrhiza DOI Creative Commons
Yujie Shi, Ping Li, Jian Sun

et al.

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

Citations

0
The first complete mitochondrial genome of Eucommia ulmoides: a multi-chromosomal architecture and controversial phylogenetic relationship in asterids DOI Creative Commons
Meng Li, Weijie Zhao, Jing Qiu

et al.

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

Published: May 29, 2025

Eucommia ulmoides (E. ulmoides) is the sole representative of Eucommiaceae family, exhibiting abundant medical application as traditional Chinese medicine and high commercial a hardy rubber tree. Although some high-quality nuclear genomes plastid (plastome) have been reported, comprehensive analysis its complete mitochondrial genome (mitogenome) remains lacking. In this study, we successfully assembled first mitogenome E. based on PacBio HiFi sequencing data. The architecture exhibited two circular chromosomes (MC1 MC2) with combined length 541.7 kb. A total 61 genes were annotated in mitogenome, including 38 unique protein-coding (PCGs), 21 tRNA genes, 2 rRNA genes. We found that dispersed repetitive sequences comprised 21.67% largest repeat spanning > 16 collinearity other species was relatively low longest homologous sequence being only 5,960 bp. phylogenetic trees constructed mitogenomes plastomes, respectively, consistently confirmed belongs to basal lamiid clade, which congruent APG IV classification system. PCG composition across four major lineages land plants (liverworts, ferns, gymnosperms, angiosperms) demonstrated convergent reduction mitogenomic evolution. reported latest two-circular chromosomal obtained through reads, genus order Garryales be described detail. provided solid foundation for comprehending evolutionary trajectories elucidating underlying causes cytonuclear discordance ulmoides.

Language: Английский

Citations

0
Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica DOI
Jiewei Zhang, Guiming Liu, Jianhua Wei

et al.

Planta, Journal Year: 2024, Volume and Issue: 260(1)

Published: June 8, 2024

Language: Английский

Citations

3
The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata DOI Creative Commons
Yujie Shi, Zhen Chen,

Jingyong Jiang

et al.

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

Published: Sept. 3, 2024

Lindera aggregata , a member belongs to the genus of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands years. However, its mitochondrial genome has not explored. Our aim is sequence assemble mitogenome L. elucidate genetic mechanism evolutionary pathway. The results had shown that was extremely complex unique multi-branched conformation with total size 912,473 bp. Comprehensive analysis protein coding genes 7 related species showed there were 40 common in their mitogenome. Interestingly, positive selection become an important factor evolution ccmB ccmFC rps10 rps11 rps7 genes. Furthermore, our data highlighted repeated trend homologous fragment migrations between chloroplast organelles, 38 fragments identified. Phylogenetic identified tree basically consistent phylogeny Laurales described APG IV system. To sum up, this study will be helpful population genetics species.

Language: Английский

Citations

2
The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies DOI Creative Commons
Lin Li,

Huizhen Fu,

Muhammad Ahsan Altaf

et al.

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

Published: Nov. 11, 2024

Pepper (Capsicum pubescens), one of five domesticated pepper species, has unique characteristics, such as numerous hairs on the epidermis its leaves and stems, black seeds, vibrant purple flowers. To date, no studies have reported complete assembly mitochondrial genome (mitogenome) C. pubescens. Understanding mitogenome is crucial for further research

Language: Английский

Citations

2