The complete mitochondrial genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales)

Choi, Seung Se; Min, Juhyeon; Kwon, Woochan; Park, Jongsun

doi:10.1080/23802359.2021.1882892

Cited by 6 publications

(3 citation statements)

References 16 publications

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“…Newly assembled organellar genomes have identical gene order, structure, and content as previously published genomes assembled using short-reads technology. e consensus sequences of organellar genomes of Riccia fluitans, Aneura pinguis, Apopellia endiviifollia, and plastome of Scapania undulata differ by only a few SNPs from previously published (Ciborowski et al, 2022;Min et al, 2020;Myszczyński et al, 2017;Sawicki et al, 2020Sawicki et al, , 2021 and newly assembled mitogenome of Scapania undulata share the genomic features with S. ampliata (Choi et al, 2021) and S. ornithopodioides (Dong et al, 2019). e mitogenomes of liverworts are characterized by low variation at a generic level, at least considering their structure, gene, and intron content, but this observation is based on limited resources since only a few genera were analyzed (Myszczyński et al, 2017;Ślipiko et al, 2022).…”

Section: Discussionmentioning

confidence: 80%

Nanopore sequencing of organellar genomes revealed heteroplasmy in simple thalloid and leafy liverworts

Sawicki,

Krawczyk,

Kurzyński

et al. 2023

Acta Soc Bot Pol

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Membrane-bound organelles, such as mitochondria and chloroplasts, have played a crucial role in the evolution of plant cells. In this study, we investigate the presence of heteroplasmy and genomic variation in liverworts, a group of non-vascular plants, using nanopore sequencing technology. We selected four liverwort species representing different lineages: Riccia fluitans, Apopellia endiviifolia, Aneura pinguis, and Scapania undulata. Through nanopore sequencing, we sequenced, assembled, and annotated the organellar genomes of selected liverwort species. The plastid genomes of Riccia fluitans, Apopellia endiviifolia, Aneura pinguis, and Scapania undulata exhibited high conservation with previously published genomes, while the mitogenome of Scapania undulata represents the first report for this species. The analysis of the liverwort organellar genomes revealed conserved gene content, structure, and order. We further investigated heteroplasmy within the liverwort species. The plastome analysis did not detect structural heteroplasmy, which is observed in some angiosperms but seems limited to seed plants. However, in the mitogenomes, we found evidence of heteroplasmy in Aneura pinguis, Apopellia endiviifolia, and Scapania undulata. The heteroplasmic sites in the mitogenomes were mainly represented by substitutions, indels, and short tandem repeat polymorphisms. Some of the identified substitutions resembled RNA editing patterns observed in liverworts. This study highlights the utility of nanopore sequencing for studying organellar genomes and detecting heteroplasmy in liverworts. The findings expand our understanding of organellar genomic variation in non-vascular plants and provide insights into the mechanisms underlying heteroplasmy in liverwort mitogenomes. Further research is needed to explore the functional significance of heteroplasmy and its implications for liverwort evolution and adaptation.

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Section: Discussionmentioning

confidence: 80%

Nanopore sequencing of organellar genomes revealed heteroplasmy in simple thalloid and leafy liverworts

Sawicki,

Krawczyk,

Kurzyński

et al. 2023

Acta Soc Bot Pol

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“…The mitogenome of Aneura pinguis counted 953 SNPs and 1940 indels [ 67 ], whereas in genus Orthotrichum s.l., 427 SNPs and 6 indels were found [ 71 ]. The species Scapania ampliata , belonging like the Calypogeia species to leafy liverworts, was detected to have 823 SNPs and 2242 indels in the mitochondrial genome [ 72 ]. Meanwhile, species belonging to the complex thalloids showed a much lower level of genetic variation in this organelle genome.…”

Section: Discussionmentioning

confidence: 99%

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

Ślipiko

Myszczyński

Buczkowska

et al. 2022

IJMS

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Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be ‘the Holy Grail’; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

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“…Assembled sequences were modified and confirmed by BWA v0.7.17 (Li, 2013) and SAMtools v1.9 (Li et al, 2009). All bioinformatic analyses were conducted in the Genome Information System (http://geis.infoboss.co.kr/) like the previous studies (Kwon et al, 2019a(Kwon et al, , 2019bPark et al, 2019aPark et al, , 2019dPark et al, , 2020bMin et al, 2020;Choi et al, 2021aChoi et al, , 2021b *Author for correspondence: starflr@infoboss.co.kr http://e-kjpt.org, © 2021 the Korean Society of Plant Taxonomists. This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.…”

Section: Dna Extraction and Mitochondrial Genome Determinationmentioning

confidence: 99%

The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea

Park¹,

Xi²,

Kim

2021

Korean J. Pl. Taxon

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Arabidopsis thaliana (L.) Heynh. is a small plant species that serves as a model organism of plant biology and genetics. Here, we present the first complete mitochondrial genome of Korean A. thaliana natural isolate (named as 180404IB4), which is 368,875 bp long and contains 58 genes (33 protein-coding genes, 22 tRNAs, and three rRNAs), with a GC ratio of 44.8%. Sixty-four single-nucleotide polymorphisms and 11 insertion and deletion regions (1,089 bp in length) are identified against the Col-0 ecotype, showing one large insertion of 1,069 bp without structural variation. Phylogenetic trees constructed from 30 conserved genes indicate that the 180404IB4 mitochondrial genome is clustered with Col-0 and three East Asian ecotypes.

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The complete mitochondrial genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales)

Cited by 6 publications

References 16 publications

Nanopore sequencing of organellar genomes revealed heteroplasmy in simple thalloid and leafy liverworts

Nanopore sequencing of organellar genomes revealed heteroplasmy in simple thalloid and leafy liverworts

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea

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