Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata

Cao, Yu; Yin, Dengpan; Pang, Bo; Li, Haibo; Liu, Qiao; Zhai, Yufeng; Ma, Nan; Shen, Hongjun; Jia, Qiaojun; Wang, Dekai

doi:10.1007/s10142-023-01223-9

Cited by 3 publications

(4 citation statements)

References 62 publications

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“…The GC content, which is an important indicator for species evaluation, is typically stable at 43%-46% in higher plants [45,46]. In this study, the GC content of I. macrocarpa was 45.53%, which is similar to other angiosperm mitogenomes [47,48]. The result supports the conclusion that GC content is highly conserved in higher plants.…”

Section: Characterization Of the I Macrocarpa Mitogenomesupporting

confidence: 86%

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex macrocarpa

Wang,

Sun,

Shi

et al. 2023

Forests

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The plant mitochondrial genome (mitogenome) has a complex organization and carries genetic traits of value in exploiting genetic resources. In this study, the Ilex macrocarpa mitogenome was sequenced and assembled to understand the genetic diversity and phylogenetic relationship. The mitogenome has a cyclic molecular structure and is 539,461 bp long with a GC content of 45.53%. It contained 39 protein-coding proteins, 19 tRNA genes, and 3 rRNA genes. The 146 simple sequence repeats and 591 dispersed repeat sequences were identified in the mitogenome. Codon usage analysis revealed a preference for codons ending in A/T. A total of 517 C to U RNA editing sites were predicted, with nad4 and ccmB being edited most frequently (39 times). Phylogenetic analysis via mitochondrial protein-coding genes showed that the Aquifoliales order contains sister plants to Lamiales, Solanales, and Gentianales. In addition, the conflicts between chloroplast and mitochondrial phylogeny were also observed. This study provides a theoretical framework for understanding the evolution, classification, and identification of the Ilex genus, which lays an important foundation for future molecular breeding investigations.

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Section: Characterization Of the I Macrocarpa Mitogenomesupporting

confidence: 86%

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex macrocarpa

Wang,

Sun,

Shi

et al. 2023

Forests

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“…The Phylloglossum mitochondrial genome (Figure 2) at 363 297 bp is smaller than the mitochondrial genomes of P. squarrosus (413 530 bp) (Liu et al, 2012) and H. crispata (412 594 bp) (Cao et al, 2023). The Phylloglossum mitochondrial genome includes 37 protein-coding genes, 3 rRNA genes and 26 tRNA genes.…”

Section: The Mitochondrial Genome Of P Drummondiimentioning

confidence: 96%

“…Organisms that contain only a handful of editing sites facilitate the identification of the specificity factors that are involved, as exemplified by Physcomitrium patens for C-to-U editing (Ichinose et al, 2013(Ichinose et al, , 2014Schallenberg-R€ udinger et al, 2013;Schallenberg-R€ udinger & Knoop, 2016;Sugita et al, 2013). It was the prediction that P. squarrosus mitochondria might only exhibit four U-to-C editing events (Cao et al, 2023;Liu et al, 2012) that prompted us to take a close look at RNA editing in P. drummondii. In their analysis of the P. squarrosus mitochondrial genome, Liu et al…”

Section: Rna Editing In Lycophytesmentioning

confidence: 99%

“…Plant models with small 'editomes' often prove more useful, with one of the most successful models for studying C-to-U editing factors being the moss Physcomitrium patens with only 11 C-to-U RNA editing events, all of which have been characterized (Ichinose et al, 2013(Ichinose et al, , 2014Schallenberg-R€ udinger et al, 2013;Schallenberg-R€ u dinger & Knoop, 2016;Sugita et al, 2013). Huperzioideae may be useful models for studying natural U-to-C editing as U-to-C editing is absent in their chloroplast genomes, and there are only a handful of U-to-C RNA editing sites predicted in published Huperzioideae mitochondrial genomes such as Phlegmariurus squarrosus (formerly Huperzia squarrosa) and Huperzia crispata (Cao et al, 2023;Liu et al, 2012). Phylloglossum is a close relative of Phlegmariurus and Huperzia; thus, we hypothesized that it would have similarly low levels of U-to-C RNA editing and would make an attractive model for studying U-to-C editing and U-to-C editing factors.…”

Section: Introductionmentioning

confidence: 99%

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Insights into U‐to‐C RNA editing from the lycophyte Phylloglossum drummondii

Kwok van der Giezen,

Viljoen,

Campbell‐Clause

et al. 2024

The Plant Journal

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SUMMARYThe lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C‐to‐U editing events in both organelles, we found just four U‐to‐C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U‐to‐C RNA editing enzymes. Four putative U‐to‐C editing factors could be matched to the four mitochondrial U‐to‐C editing sites. Due to the unusually few numbers of U‐to‐C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.

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Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species

Sun,

Han,

Wang

et al. 2024

Front. Plant Sci.

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Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

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Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata

Cited by 3 publications

References 62 publications

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex macrocarpa

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex macrocarpa

Insights into U‐to‐C RNA editing from the lycophyte Phylloglossum drummondii

Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species

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