Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops

Xia, Lei; Cheng, Chunyan; Zhao, Xiaokun; He, Xiaolu; Yu, Xiaqing; Li, Ji; Wang, Yuhui; Chen, Jinfeng

doi:10.1016/j.gene.2022.146342

Cited by 6 publications

(3 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…GC content is also one of the important indicators for species evaluation, and C. acerifolia mitogenome GC content was 46.91%, which is similar to the GC content of the mitogenomes of most angiosperms (Q. acutissima, 45.72%; Dalbergia odorifera, 45.1%, Cucumis hystrix, 44.59%; Elymus sibiricus; 44.47%) and higher than that of the clematis chloroplast genome (37.87-38.19%) (Hong et al, 2021;Liu et al, 2022;Xia et al, 2022). The C. acerifolia mitogenome exhibits a multi-branched structure (linear molecule 1 and circular molecule 2), and the vast majority of published plant mitogenomes are presented as circular DNA molecules, and there are also conformational forms such as Y-and H-type linear, but mitochondrial DNA in its real state is often a mixture of different conformational forms (Backert and Börner, 2000;Kitazaki and Kubo, 2010;Bonen, 2014;Christensen, 2019).…”

Section: Discussionmentioning

confidence: 67%

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Liu

Yuan

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.

show abstract

Section: Discussionmentioning

confidence: 67%

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Liu

Yuan

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Mitochondrial genomes provide important genetic information for phylogenetic studies of different species ( Xia et al., 2022 ). The ML tree inferred from 9 conserved mitochondrial PCG genes of 29 species from 19 families revealed that six Ranunculales species ( Liriodendron tulipifera , Aconitum kusnezoffii , Anemone maxima , C. chinensis , C. deltoidea , and C. omeiensis ) clustered closely together into one clade ( Supplementary Figure S6 ).…”

Section: Resultsmentioning

confidence: 99%

“…In contrast, the mitochondrial genomes of angiosperms evolve very rapidly in terms of structural rearrangements and gene transfer ( Gualberto and Newton, 2017 ). The significant variation and different gene orders may occur within closely related species ( Van de Paer et al., 2018 ), for example, within Cucumis (Cucurbitaceae) ( Xia et al., 2022 ), Monsonia (Geraniaceae) ( Cole et al., 2018 ), Mangifera (Anacardiaceae) ( Niu et al., 2022 ). The high complexity of the plant mitochondrial genome makes it difficult to sequence and assemble.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the complete mitochondrial genomes of three Coptis species (C. chinensis, C. deltoidea and C. omeiensis): the important medicinal plants in China

Zhong

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

Coptis plants (Ranunculaceae) contain high levels of isoquinoline alkaloids and have a long history of medicinal use. Coptis species are of great value in pharmaceutical industries and scientific research. Mitochondria are considered as one of the central units for receiving stress signals and arranging immediate responses. Comprehensive characterizations of plant mitogenomes are imperative for revealing the relationship between mitochondria, elucidating biological functions of mitochondria and understanding the environmental adaptation mechanisms of plants. Here, the mitochondrial genomes of C. chinensis, C. deltoidea and C. omeiensis were assembled through the Nanopore and Illumina sequencing platform for the first time. The genome organization, gene number, RNA editing sites, repeat sequences, gene migration from chloroplast to mitochondria were compared. The mitogenomes of C. chinensis, C. deltoidea and C. omeiensis have six, two, two circular-mapping molecules with the total length of 1,425,403 bp, 1,520,338 bp and 1,152,812 bp, respectively. The complete mitogenomes harbors 68-86 predicted functional genes including 39-51 PCGs, 26-35 tRNAs and 2-5 rRNAs. C. deltoidea mitogenome host the most abundant repeat sequences, while C. chinensis mitogenome has the largest number of transferred fragments from its chloroplasts. The large repeat sequences and foreign sequences in the mitochondrial genomes of Coptis species were related to substantial rearrangements, changes in relative position of genes and multiple copy genes. Further comparative analysis illustrated that the PCGs under selected pressure in mitochondrial genomes of the three Coptis species mainly belong to the mitochondrial complex I (NADH dehydrogenase). Heat stress adversely affected the mitochondrial complex I and V, antioxidant enzyme system, ROS accumulation and ATP production of the three Coptis species. The activation of antioxidant enzymes, increase of T-AOC and maintenance of low ROS accumulation in C. chinensis under heat stress were suggested as the factors for its thermal acclimation and normal growth at lower altitudes. This study provides comprehensive information on the Coptis mitogenomes and is of great importance to elucidate the mitochondrial functions, understand the different thermal acclimation mechanisms of Coptis plants, and breed heat-tolerant varieties.

show abstract

The CsPPR gene with RNA-editing function involved in leaf color asymmetry of the reciprocal hybrids derived from Cucumis sativus and C. hystrix

Xia,

Wang,

Zhao

et al. 2024

Planta

View full text Add to dashboard Cite

Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops

Cited by 6 publications

References 46 publications

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Comprehensive analysis of the complete mitochondrial genomes of three Coptis species (C. chinensis, C. deltoidea and C. omeiensis): the important medicinal plants in China

The CsPPR gene with RNA-editing function involved in leaf color asymmetry of the reciprocal hybrids derived from Cucumis sativus and C. hystrix

Contact Info

Product

Resources

About