Geochemical alkalinity and acidity as preferential site-specific for three lineages liverwort of Aneura pinguis cryptic species A

Bączkiewicz, Alina; Diatta, Jean; Drapikowska, Maria; Rodkiewicz, Patrycja; Sawicki, Jakub; Szczecińska, Monika; Buczkowska, Katarzyna

doi:10.1038/s41598-021-83553-x

Cited by 3 publications

(1 citation statement)

References 19 publications

(23 reference statements)

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“…Another cryptic species of simple thalloid liverwort, Aneura pinguis , has been more thoroughly studied, but despite the presence of various lineage-specific DNA markers 3 , 67 , 92 and many biochemical compounds 93 , it lacks significant morpho-anatomical differentiation. Furthermore, the cryptic lineages of A. endiviifolia and some of A. pinguis differ in their preferred microhabitats, which can be characterised not only by general ecological descriptions, but also by specific parameters such as pH and concentrations of calcium, magnesium, potassium, and sodium 94 .…”

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confidence: 99%

The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage

Paukszto,

Górski,

Krawczyk

et al. 2023

Sci Rep

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Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.

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Section: Discussionmentioning

confidence: 99%

The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage

Paukszto,

Górski,

Krawczyk

et al. 2023

Sci Rep

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Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

et al. 2021

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The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

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Comparative Analysis of Apopellia endiviifolia Plastomes Reveals a Strikingly High Level of Differentiation between Its Terrestrial and Water Form

et al. 2021

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The simple thalloid liverwort Apopellia endiviifolia is a widespread Holarctic species belonging to the family Pelliaceae. European populations of this species comprise two distinct evolutionary lineages named “species A”, known also as water form, and typical, mainly terrestrial forms named “species B”. Newly sequenced, assembled and annotated chloroplast genomes of six European specimens belonging to the two cryptic lineages occupying different microhabitats, revealed the structure typical for liverworts and previously sequenced reference. The plastomes of A. endiviifolia are 120,537–120,947 bp long with a structure typical for most plants, including a pair of IR regions (each of 9092–9207 bp) separated by LSC (82,506–82,609 bp) and SSC (19,854–19,924 bp) regions and consist of 121 unique genes, including 81 protein-coding genes, 6 genes of unknown function (ycf genes), 4 ribosomal RNAs and 30 transfer RNAs. Comparative analysis of typical, terrestrial and water forms revealed 4971 molecular diagnostic characters (MDCs), which exceeds numbers found in many well recognized liverworts taxa. Moreover, beside the presence of evolutionary hotspots like ycf1 and ycf2 genes and several intergenic spacer like ndhB-psbM, rps4-ndhJ and ndhC-atpE, the molecular identification of Apopellia cryptic species was possible by almost 98% of 500 bp long frames simulating mini barcodes. The different ecological niches can be driven by different pressures of positive selection, which was detected in nine genes including ccsA, ndhD, ndhF, petA, psbB, psbC, rpoB, ycf1 and ycf2. Despite clearly genetic differences and ecological preferences, the current observation of morphological differentiation does not no allow to separate terrestrial and water forms into taxonomic species.

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Geochemical alkalinity and acidity as preferential site-specific for three lineages liverwort of Aneura pinguis cryptic species A

Cited by 3 publications

References 19 publications

The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage

The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage

Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Comparative Analysis of Apopellia endiviifolia Plastomes Reveals a Strikingly High Level of Differentiation between Its Terrestrial and Water Form

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