Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes

Ślipiko, Monika; Myszczyński, Kamil; Buczkowska, Katarzyna; Bączkiewicz, Alina; Szczecińska, Monika; Sawicki, Jakub

doi:10.21203/rs.2.17612/v2

Cited by 3 publications

(3 citation statements)

References 84 publications

(62 reference statements)

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“…Most of the identified intergeneric regions are too short to be recommended as barcodes, but these six highly variable coding regions may be suitable for future infrafamilial phylogenetic analysis. Indeed, the abovementioned six coding regions previously have been identified as highly variable regions in many plant species (Fan et al., 2018; Machado et al., 2020; Wu et al., 2018; Ye et al., 2018; Zhang et al., 2020), as well as in the liverwort genus Calypogeia Arnell (Ślipiko et al., 2020).…”

Section: Discussionmentioning

confidence: 99%

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

et al. 2022

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Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well‐known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well‐conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.

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Section: Discussionmentioning

confidence: 99%

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

et al. 2022

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“…Since complete plastome and nrDNA arrays were proposed to be the next generation DNA barcodes for plant species identification (Coissac et al, 2016; Hollingsworth et al, 2016; Kane et al, 2012; Kane & Cronk, 2008; Li et al, 2015; Nock et al, 2011), much advancement has gone into molecular species identification of taxonomically difficult taxa, such as Panax (Araliaceae) with 70% of species discriminated (Ji et al, 2019), and Taxus (Taxaceae) with all species (100%) discriminated (Fu et al, 2019). Despite a steep increase in super‐barcode‐related studies (Chen et al, 2022; Dong et al, 2021; Ślipiko et al, 2020; Wang et al, 2018), the discriminatory power of super‐barcodes remains controversial. Some studies argue that the power of super‐barcodes as a species identification tool is quite limited (Krawczyk et al, 2018; Liu et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Jiang

Folk

et al. 2022

Molecular Ecology Resources

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Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as “super‐barcodes,” might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super‐barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super‐barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH‐psbA, nrITS) and super‐barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets—the lowest estimated rate of super‐barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super‐barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.

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“…Using comparison of Panax species, the intron of rps16 and two regions of ycf1 gene were developed as specific DNA barcodes (Dong et al, 2014). Furthermore, the ndhB and ndhH genes and the trnT‐trnL spacer identified Calypogeia species with high success rates (Ślipiko et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

Dong

Sun

Liu

et al. 2021

J of Sytematics Evolution

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The olive genus Olea includes c. 30-40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Oleaspecific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.

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Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes

Cited by 3 publications

References 84 publications

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

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