Seasonal Variability of Volatile Components in Calypogeia integristipula

Liverworts contain a large number of biologically active compounds that are synthesised and stored in their oil bodies. However, knowledge about the chemical composition of individual species is still incomplete. The subject of the study was Calypogeia integristipula, a species representing leafy liverworts. Plant material for chemotaxonomic studies was collected from various locations in Poland. The chemical composition was determined in 74 samples collected from the natural environment in 2021 and 2022 in three growing seasons: spring, summer and autumn, and for comparison with samples originating from in vitro culture. The plants were classified as Calypogeia integristipula on the basis of morphological characteristics, oil bodies, and DNA markers. The volatile organic compounds (VOCs) from the biological material were extracted by headspace solid phase microextraction (HS-SPME). The samples were then analysed by gas chromatography-mass spectrometry (GC-MS). A total of 79 compounds were detected, of which 44 compounds were identified. The remaining compounds were described using the MS fragmentation spectrum. Cyclical changes in the composition of compounds associated with the growing season of Calypogeia integristipula were observed. Moreover, samples from in vitro culture and samples taken from the natural environment were shown to differ in the composition of chemical compounds. In terms of quantity, among the volatile compounds, compounds belonging to the sesquiterpene group (46.54-71.19%) and sesqiuterpenoid (8.12-22.11%) dominate. A smaller number of compounds belong to aromatic compounds (2.30-10.96%), monoterpenes (0.01-0.07%), monoterpenoids (0.02-0.33%), and aliphatic hydrocarbons (1.11-6.12%). The dominant compounds in the analysed liverworts were: anastreptene (15.27-31.14%); bicyclogermacrene (6.99-18.09%), 4,5,9,10-dehydro-isolongifolene (2.00-8.72%), palustrol (4.95-9.94%), spathulenol (0.44-5.11%).

Chemical Fingerprinting of Cryptic Species and Genetic Lineages of Aneura pinguis (L.) Dumort. (Marchantiophyta, Metzgeriidae)

Aneura pinguis (L.) Dumort. is a representative of the simple thalloid liverworts, one of the three main types of liverwort gametophytes. According to classical taxonomy, A. pinguis represents one morphologically variable species; however, genetic data reveal that this species is a complex consisting of 10 cryptic species (named by letters from A to J), of which four are further subdivided into two or three evolutionary lineages. The objective of this work was to develop an efficient method for the characterisation of plant material using marker compounds. The volatile chemical constituents of cryptic species within the liverwort A. pinguis were analysed by GC-MS. The compounds were isolated from plant material using the HS-SPME technique. Of the 66 compounds examined, 40 were identified. Of these 40 compounds, nine were selected for use as marker compounds of individual cryptic species of A. pinguis. A guide was then developed that clarified how these markers could be used for the rapid identification of the genetic lineages of A. pinguis. Multivariate statistical analyses (principal component and cluster analysis) revealed that the chemical compounds in A. pinguis made it possible to distinguish individual cryptic species (including genetic lineages), with the exception of cryptic species G and H. The classification of samples based on the volatile compounds by cluster analysis reflected phylogenetic relationships between cryptic species and genetic lineages of A. pinguis revealed based on molecular data.

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

BACKGROUND

Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification.

RESULTS

On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%.

CONCLUSIONS

This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.

The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes

The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.

Does Calypogeia azurea (Calypogeiaceae, Marchantiophyta) occur outside Europe? Molecular and morphological evidence

Oil bodies are the unique feature of most liverworts. Their shape, color and distribution pattern in leaf and underleaf cells are important taxonomic features of the genus Calypogeia. Most species of the genus Calypogeia have pellucid and colorless oil bodies, whereas colored, including gray to pale brown, purple-brown or blue oil bodies, are rare. To date, C. azurea was the only species with blue oil bodies to have been considered as a species of the Holarctic range. This species has been noted in various parts of the northern hemisphere-from North America, through Europe to the Far East. The aim of this study was to determine the genetic diversity of C. azurea from different parts of its distribution range and to ascertain whether blue oil bodies appeared once or several times in the evolution of the genus Calypogeia. The phylogenetic analyses based on four plastid regions (rbcL, trnG, trnL, trnH-psbA) and one nuclear region (ITS2) revealed that C. azurea is presently a paraphyletic taxon, with other Calypogeia species nested among C. azurea accessions that were clustered into four different clades. Based on the level of genetic divergence (1.03-2.17%) and the observed morphological, ecological and geographical differences, the evaluated clades could be regarded as previously unrecognized species. Four species were identified: C. azurea Stotler & Crotz (a European species corresponding to the holotype), two new species from Pacific Asia-C. orientalis Buczkowska & Bakalin and C. sinensis Bakalin & Buczkowska, and a North American species which, due to the lack of identifiable morphological features, must be regarded as the cryptic species of C. azurea with a provisional name of C. azurea species NA.

High correlation of chemical composition with genotype in cryptic species of the liverwort Aneura pinguis

Chemical constituents of cryptic species detected within the liverwort Aneura pinguis were identified using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). Fibre coating with divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) was used. A total of 48 samples of A. pinguis were analysed. The studied plants were identified genetically based on barcode DNA sequences and represented three cryptic species (A, B and F) of A. pinguis. Cryptic species A and B are genetically diverse; both represent three evolutionary lineages: A1, A2, A3 and B1, B2, B3, respectively. The cryptic species F that was recently detected is not diverse. The most characteristic compounds in analysed samples were sesquiterpene hydrocarbons (up to 17.7% for A1; 15.7% for A2; 20.6% for A3; 7.7% for B1; 2.0% for B2; 3.7% for B3; 10.2% for F), oxygenated sesquiterpenoids (up to 68.0% for A1; 54.7% for A2; 52.6% for A3; 63.5% for B1; 88.7% for B2; 82.7% for B3; 78.8% for F), and linear aliphatic hydrocarbons (up to 14.8% for A1; 1.1% for A2; 12.1% for A3; 6.9 for B1; 5.2% for B2; 1.1% for B3; 7.0% for F). The dominant compound in the studied samples was pinguisone. The second dominant compound present in the tested plant material was deoxopinguisone, except for lineage B2, where only a small relative concentration of this compound was found. A high content of deoxopinguisone in cryptic species A (lineages A1, A2 and A3) was accompanied by the presence of isopinguisone and methyl norpinguisonate, whereas these two compounds were not detected in cryptic species B (lineages B1 and B3) and F. The chemical compounds detected in the studied samples of A. pinguis were subjected to multivariate statistical analysis. The results showed that the chemical composition depends mainly on the genotype of the plant and slightly on the habitat. However, there was no clear correlation between the volatile compounds and the date of collection of the studied plants.

DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta)

Aneura pinguis is a thalloid liverwort species with broad geographical distribution. It is composed of cryptic species, however, the number of cryptic species within A. pinguis is not known. Five cpDNA regions (matK, rbcL, rpoC1, trnH-psbA and trnL-trnF) and the entire nuclear ITS region were studied in 130 samples of A. pinguis from different geographical regions. The relationships between the cryptic species of A. pinguis, A. maxima and A. mirabilis were analyzed. All of the examined samples were clustered into 10 clades corresponding to 10 cryptic species of A. pinguis (marked A to J). Aneura mirabilis and A. maxima were nested among different cryptic species of A. pinguis, which indicates that A. pinguis is a paraphyletic taxon. Subgroups were found in cryptic species A, B, C and E. As single barcodes, all tested DNA regions had 100% discriminant power and fulfilled DNA barcode criteria for species identification; however, the only combination detected in all subgroups was trnL-trnF with trnH-psbA or ITS2. The distances between cryptic species were 11- to 35-fold higher than intraspecific distances. In all analyzed DNA regions, the distances between most pairs of cryptic A. pinguis species were higher than between A. maxima and A. mirabilis. All cryptic species of A. pinguis clearly differed in their habitat preferences, which suggests that habitat adaptation could be the main driving force behind cryptic speciation within this taxon.

The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants

Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex. The chloroplast genome with the nucleotide diversity 0.05111 and 1537 indels is by far more variable than mitogenome with π value 0.00233 and number of indels 1526. Tests of selection evidenced that on about 36% of chloroplast genes and on 10% of mitochondrial genes of A. pinguis acts positive selection. It suggests an advanced speciation of species. The phylogenetic analyses based on genomes show that A. pinguis is differentiated and forms three distinct clades. Moreover, on the cpDNA trees, Aneura mirabilis is nested among the cryptic species of A. pinguis. This indicates that the A. pinguis cryptic species do not derive directly from one common ancestor.

Geographic distribution and new localities for cryptic species of the Aneura pinguis complex and Aneura maxima in Poland

The genus Aneura is represented in Poland by two species - A. pinguis and A. maxima. A. pinguis in contrast to A. maxima is a complex of cryptic species temporarily named A. pinguis species: A, B, C, and E. All species of the A. pinguis complex and A. maxima differ in their geographic distribution and habitat preferences. A. pinguis species A grows mainly on humus over limestone rocks in the Western Carpathians, A. pinguis species B occurs mainly on clay soil in Bieszczady Mts. and in clayish areas of lowlands, A. pinguis species C grows both in lowlands and mountains and it occupies mostly wet sandy soils, on the shores of oligotrophic lakes and river and mountain stream banks, A. pinguis species E is connected with calcareous rocks in flowing water in mountains. A. maxima grows over the country - both in lowlands and mountains, in marshes situated on the river banks.

Genetic studies revealed differences between European and North American populations of Calypogeia azurea

Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

Two ploidy levels of genetically delimited groups of the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae)

Calypogeia fissa is a suboceanic-mediterrean and amphiatlantic species, which comprises two subspecies: C. fissa subsp. fissa occurring in Europe and C. fissa subsp. neogea Schust. known from North America. Recently, within the European part of distribution, three groups (PS, PB and G) were distinguished with the aid of genetic and molecular markers. The flow cytometry results revealed that two of the detected groups of the European C. fissa, which are frequent in Poland (PS and PB), differ in ploidy level: the PS group is haploid, whereas the PB group is diploid. Isozyme pattern at two loci may suggest an allopolyploid origin of the diploid PB group.

The complete mitochondrial genome of the cryptic species C of Aneura pinguis

The structure of the Aneura pinguis mitochondrial genome (GenBank accession no. NC_026901) is similar to that of closely related Metzgeriales species: it has a total length of 165 603 bp, the base composition of the mitogenome is the following: A (26.2%), C(23.6%), G(23.8%), and T(26.4%). The A. piguis mitochondrial genome contains 69 genes. A complete mitochondrial genome sequence of A. pinguis will help better to understand mitogenome structure and content among Metzgeriales order.

Volatile compounds in cryptic species of the Aneura pinguis complex and Aneura maxima (Marchantiophyta, Metzgeriidae)

Aneura pinguis is one of the liverwort species complexes that consist of several cryptic species. Ten samples collected from different regions in Poland are in the focus of our research. Eight of the A. pinguis complex belonging to four cryptic species (A, B, C, E) and two samples of closely related species Aneura maxima were tested for the composition of volatile compounds. The HS-SPME technique coupled to GC/FID and GC/MS analysis has been applied. The fiber coated with DVB/CAR/PDMS has been used. The results of the present study, revealed the qualitative and quantitative differences in the composition of the volatile compounds between the studied species. Mainly they are from the group of sesquiterpenoids, oxygenated sesquiterpenoids and aliphatic hydrocarbons. The statistical methods (CA and PCA) showed that detected volatile compounds allow to distinguish cryptic species of A. pinguis. All examined cryptic species of the A. pinguis complex differ from A. maxima. Species A and E of A. pinguis, in CA and PCA, form separate clusters remote from two remaining cryptic species of A. pinguis (B and C) and A. maxima. Relationship between the cryptic species appeared from the chemical studies are in accordance with that revealed on the basis of DNA sequences.