TrnL- trnF intergenic spacer and trnL intron define major clades within Luzula and Juncus (Juncaceae): importance of structural mutations

Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae

Juncaceae is a cosmopolitan family belonging to the cyperid clade of Poales together with Cyperaceae and Thurniaceae. These families have global economic and ethnobotanical significance and are often keystone species in wetlands around the world, with a widespread cosmopolitan distribution in temperate and arctic regions in both hemispheres. Currently, Juncaceae comprises more than 474 species in eight genera: Distichia, Juncus, Luzula, Marsippospermum, Oreojuncus, Oxychloë, Patosia and Rostkovia. The phylogeny of cyperids has not been studied before in a complex view based on most sequenced species from all three families. In this study, most sequenced regions from chloroplast (rbcL, trnL, trnL-trnF) and nuclear (ITS1-5.8S-ITS2) genomes were employed from more than a thousand species of cyperids covering all infrageneric groups from their entire distributional range. We analyzed them by maximum parsimony, maximum likelihood, and Bayesian inference to revise the phylogenetic relationships in Juncaceae and Cyperaceae. Our major results include the delimitation of the most problematic paraphyletic genus Juncus, in which six new genera are recognized and proposed to recover monophyly in this group: Juncus, Verojuncus, gen. nov., Juncinella, gen. et stat. nov., Alpinojuncus, gen. nov., Australojuncus, gen. nov., Boreojuncus, gen. nov. and Agathryon, gen. et stat. nov. For these genera, a new category, Juncus supragen. et stat. nov., was established. This new classification places most groups recognized within the formal Juncus clade into natural genera that are supported by morphological characters.

Synopsis of the order Juncales (Liliopsida) in Ukraine

Juncales is an order of vascular plants with cosmopolitan distribution. Two families of Juncales are present in flora of Ukraine: Juncaceae and Cyperaceae. Through 1985–2021, we conducted comprehensive revision of Juncales in Ukraine. The aim of this research was to compile a checklist of Juncales species in the flora of Ukraine. Our research is based on herbarium materials, literature data and field trips. We collected data in many herbariums of Ukraine and other countries. Our understanding of the taxa was further supplemented by field observations in mountainous (Carpathians and Crimea) and plain territories of Ukraine. Also, we collected information about Juncales species from numerous literature sources. For each taxon, we provided nomenclatural citation and basic synonyms. According to our data, the order Juncales in the flora of Ukraine contains 188 species, belonging to 19 genera. Lists of Juncales species can be found in many thorough publications. For a long time, Checklist of Mosyakin & Fedoronchuk (1999) was the main list in the nomenclature of vascular plants in Ukraine. To date, many nomenclature and taxonomic changes have been accumulated. For example, we accept genera Schoenoplectiella and Oreojuncus here. Researchers have found many new species for the territory of Ukraine. This information can be found in numerous publications, but is fragmented. Therefore, we have compiled an updated summary of the Juncales species. In Ukrainian territory, Juncales species are considered both widespread and rare. We refer to the rarest species Carex alba, C. bicolor, C. bohemica, C. brunnescens, C. buxbaumii, C. depauperata, C. fuliginosa, C. globularis, C. heleonastes, C. lachenalii, C. loliacea, C. obtusata, C. pediformis, C. rupestris, C. strigosa, Cyperus longus, Eleocharis multicaulis, E. oxylepis, Fimbristylis bisumbellata, Juncus acutiflorus, J. soranthus, J. subnodulosus, Isolepis setacea, Luzula spicata, Schoenoplectus pungens, Trichophorum alpinum, T. cespitosum. Also, the following species are rare: Bolboschoenus yagara, Carex chordorrhiza, C. davalliana, C. dioica, C. hostiana, C. pauciflora, C. secalina, C. vaginata, Cladium mariscus, Eleocharis carniolica, Juncus capitatus, J. castaneus, J. littoralis, J. sphaerocarpus, J. thomasii, J. triglumis, Luzula alpinopilosa, L. sudetica, Schoenoplectiella mucronata, Schoenus ferrugineus.

Synopsis of the order Juncales (Liliopsida) in Ukraine

Juncales is an order of vascular plants with cosmopolitan distribution. Two families of Juncales are present in flora of Ukraine: Juncaceae and Cyperaceae. Through 1985–2021, we conducted comprehensive revision of Juncales in Ukraine. The aim of this research was to compile a checklist of Juncales species in the flora of Ukraine. Our research is based on herbarium materials, literature data and field trips. We collected data in many herbariums of Ukraine and other countries. Our understanding of the taxa was further supplemented by field observations in mountainous (Carpathians and Crimea) and plain territories of Ukraine. Also, we collected information about Juncales species from numerous literature sources. For each taxon, we provided nomenclatural citation and basic synonyms. According to our data, the order Juncales in the flora of Ukraine contains 188 species, belonging to 19 genera. Lists of Juncales species can be found in many thorough publications. For a long time, Checklist of Mosyakin & Fedoronchuk (1999) was the main list in the nomenclature of vascular plants in Ukraine. To date, many nomenclature and taxonomic changes have been accumulated. For example, we accept genera Schoenoplectiella and Oreojuncus here. Researchers have found many new species for the territory of Ukraine. This information can be found in numerous publications, but is fragmented. Therefore, we have compiled an updated summary of the Juncales species. In Ukrainian territory, Juncales species are considered both widespread and rare. We refer to the rarest species Carex alba, C. bicolor, C. bohemica, C. brunnescens, C. buxbaumii, C. depauperata, C. fuliginosa, C. globularis, C. heleonastes, C. lachenalii, C. loliacea, C. obtusata, C. pediformis, C. rupestris, C. strigosa, Cyperus longus, Eleocharis multicaulis, E. oxylepis, Fimbristylis bisumbellata, Juncus acutiflorus, J. soranthus, J. subnodulosus, Isolepis setacea, Luzula spicata, Schoenoplectus pungens, Trichophorum alpinum, T. cespitosum. Also, the following species are rare: Bolboschoenus yagara, Carex chordorrhiza, C. davalliana, C. dioica, C. hostiana, C. pauciflora, C. secalina, C. vaginata, Cladium mariscus, Eleocharis carniolica, Juncus capitatus, J. castaneus, J. littoralis, J. sphaerocarpus, J. thomasii, J. triglumis, Luzula alpinopilosa, L. sudetica, Schoenoplectiella mucronata, Schoenus ferrugineus.

Identification and quantification of cassava starch adulteration in different food starches by droplet digital PCR

We report a rapid and accurate quantitative detection method using droplet digital PCR (ddPCR) technology to identify cassava adulteration in starch products. The ddPCR analysis showed that the weight of cassava (M) and cassava-extracted DNA content had a significant linear relationship-the correlation coefficient was R2 = 0.995, and the maximum coefficient of variation of replicates was 7.48%. The DNA content and DNA copy number (C) measured by ddPCR also had a linear relationship with R2 = 0.992; the maximum coefficient of variation of replicates was 8.85%. The range of cassava ddPCR DNA content was 25 ng/μL, and the formula M = (C + 32.409)/350.579 was obtained by converting DNA content into the median signal. The accuracy and application potential of the method were verified using the constructed adulteration model.

Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.

Phylogeography of Swertia perennis in Europe based on cpDNA markers

Background

Swertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species.

Methods

In this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations.

Results

A total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA.

Discussion

The lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and the origin and distribution of this species in Europe. Today, it seems to be restricted due to the occurrence of plants which clearly reflects the genetic variability from the ancient period.

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

Discovery of novel plastid phenylalanine (trnF) pseudogenes defines a distinctive clade in Solanaceae

BACKGROUND

The plastome of embryophytes is known for its high degree of conservation in size, structure, gene content and linear order of genes. The duplication of entire tRNA genes or their arrangement in a tandem array composed by multiple pseudogene copies is extremely rare in the plastome. Pseudogene repeats of the trnF gene have rarely been described from the chloroplast genome of angiosperms.

FINDINGS

We report the discovery of duplicated copies of the original phenylalanine (trnFGAA) gene in Solanaceae that are specific to a larger clade within the Solanoideae subfamily. The pseudogene copies are composed of several highly structured motifs that are partial residues or entire parts of the anticodon, T- and D-domains of the original trnF gene.

CONCLUSIONS

The Pseudosolanoid clade consists of 29 genera and includes many economically important plants such as potato, tomato, eggplant and pepper.

Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): molecular evolution of tandemly repeated structural mutations

Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5'-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3' of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3' and 5' acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.

Total centromere size and genome size are strongly correlated in ten grass species

It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat–maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.

Identification and characterization of plastid trnF(GAA) pseudogenes in four species of Solanum (Solanaceae)

Non-functional trnF pseudogenes that rarely occur in embryophytes have been found in Solanaceae. We have sequenced the trnL-F intergenic spacer of four species of Solanum, and found duplicated regions of the original trnF gene. These repeats were 94-260 bp long causing large length variation in the trnL-F intergenic spacer resulting from differences in pseudogene copy number (2-4). The duplicated trnF regions are comprised of several highly structured motifs, which were partial residues, or entire parts of the Anticodon, T- and D-domains of the original gene, but all lacked the acceptor stems at the 5'- or 3'-end. Pseudogenes included several transitions and transversions in their sequences compared to the original trnF gene. Among pseudogene copies, T-domains were more frequent and fragmented than D-domain elements. Our results demonstrate that although chloroplast evolution is uniform such structural duplications in the sequences used for phylogenetic reconstructions should be treated with great caution.

Plastidic trnFUUC pseudogenes in North American genus Boechera (Brassicaceae): mechanistic aspects of evolution

The origin and maintenance of a plastidic tandem repeat next to the TRNF (UUC) gene were analyzed in the genus BOECHERA in a phylogenetic context and were compared to published analogous examples that emerged in parallel in the Asteraceae and Juncaceae, respectively. Although we identified some features common to these taxonomic groups with respect to structure and origin of the region, obvious differences were encountered, which argue against a specific mechanism or evolutionary principle underlying the parallel origin and maintenance of the TRNF-tandem repeats in those families. In contrast to the situation in the Asteraceae, no reciprocal recombinant repeat types have been observed in the Brassicaceae. Forty copy types, classified into three groups, were isolated from 103 chloroplast haplotypes of BOECHERA and it was demonstrated that they are composed of four subregions of various origins. We discuss various mutation mechanisms such as DNA replication slippage, and inter- and intrachromosomal recombination which were reported to mediate variation in copy numbers and other types of observed sequence length polymorphism. It is shown that the observed molecular structure of the tandem repeat region did not fully fit the particular patterns expected under a scenario of evolution including any of the known mechanisms. Nevertheless, it appeared that intermolecular unequal crossing-over is most likely the driving force in the evolution of this tandem repeat. However, it remains to be explained, why no reciprocal recombinant copy types have been observed. The reconstructed phylogenetic relationships among copies reflected different evolutionary scenarios as follows: (1) A single and ancient origin of copies pre-dates the radiation of BOECHERA. (2) Parallel expansion and shortening of the tandem repeat within different BOECHERA lineages. (3) Conservation of the first copy, as it was the only one present in all chloroplast haplotypes.

Circumpolar phylogeography of Juncus biglumis (Juncaceae) inferred from AFLP fingerprints, cpDNA sequences, nuclear DNA content and chromosome numbers

We explored the circumpolar phylogeographic history of the arctic-alpine Juncus biglumis using amplified fragment length polymorphisms (AFLPs), sequences of cpDNA, relative nuclear DNA content and chromosome numbers. The analyses of the AFLP and cpDNA data gave congruent results and revealed three distinct clades. One of them, represented by a single population from the Taymyr peninsula in northern Siberia, had approximately fourfold larger genome size than the other samples and produced an AFLP pattern that was too aberrant to be analysed together with the rest of the data set. The two other clades represented different ploidy levels (2n = 60 and 120) as judged from chromosome counts of selected populations but differed only in c. 6% relative DNA content. Based on the AFLP and partly also on the cpDNA data, each of the two main clades was further subdivided into two well-supported subgroups. Three of the subgroups were widespread and exhibited largely overlapping distribution patterns. The fourth subgroup seems to be absent from the North Atlantic region and from western Siberia. We suggest that the four subgroups diverged during isolation in different glacial refugia during the Quaternary. Interestingly, individuals of both main clades were encountered in geographically close populations in eastern Greenland and even within a single population from Svalbard, indicating that both areas were colonised at least twice. The different genome sizes and ploidy levels strongly suggest that the three main clades represent distinct gene pools and act as cryptic species.

Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

Plastid sequences are among the most widely used in phylogenetic and phylogeographic studies in flowering plants, where they are usually assumed to evolve like non-recombining, uniparentally transmitted, single-copy genes. Among others, this assumption can be violated by intracellular gene transfer (IGT) within cells or by the exchange of genes across mating barriers (horizontal gene transfer, HGT). We report on HGT of a plastid region including rps2, trnL-F, and rbcL in a group of non-photosynthetic flowering plants. Species of the parasitic broomrape genus Phelipanche harbor two copies of rps2, a plastid ribosomal gene, one corresponding to the phylogenetic position of the respective species, the other being horizontally acquired from the related broomrape genus Orobanche. While the vertically transmitted copies probably reside within the plastid genome, the localization of the horizontally acquired copies is not known. With both donor and recipient being parasitic plants, a possible pathway for the exchange of genetic material is via a commonly attacked host.

Supernetwork Identifies Multiple Events of Plastid trnF(GAA) Pseudogene Evolution in the Brassicaceae

The occurrence of nonfunctional trnF pseudogenes has been rarely described in flowering plants. However, we describe the first large-scale supernetwork for the Brassiccaeae built from gene trees for 5 loci (adh, chs, matK, trnL-F, and ITS) and report multiple independent origins for trnF pseudogenes in crucifers. The duplicated regions of the original trnF gene are comprised of its anticodon domain and several other highly structured motifs not related to the original gene. Length variation of the trnL-F intergenic spacer region in different taxa ranges from 219 to 900 bp as a result of differences in pseudocopy number (1-14). It is speculated that functional constraints favor 2-3 or 5-6 copies, as found in Arabidopsis and Boechera. The phylogenetic distribution of microstructural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci.

Evolution of the trnF(GAA) Gene in Arabidopsis Relatives and the Brassicaceae Family: Monophyletic Origin and Subsequent Diversification of a Plastidic Pseudogene

Recently, we used the 5'-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions and phylogenetic analysis among the genera Arabidopsis, Boechera, Rorippa, Nasturtium, and Cardamine. Despite the fact that extensive gene duplications are rare among the chloroplast genome of higher plants, within these taxa the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with one to eight tandemly repeated copies in close 5' proximity of the functional gene. Interestingly, even in Arabidopsis thaliana we found six putative pseudogenic copies of the functional trnF gene within the 5'-intergenic trnL-trnF spacer. A reexamination of trnL(UAA)-trnF(GAA) regions from numerous published phylogenetic studies among halimolobine, cardaminoid, and other cruciferous taxa revealed not only extensive trnF gene duplications but also favor the hypothesis about a single origin of trnF pseudogene formation during evolution of the Brassicaceae family 16-21 MYA. Conserved sequence motifs from this tandemly repeated region are codistributed nonrandomly throughout the plastome, and we found some similarities with a DNA sequence duplication in the rps7 gene and its adjacent spacer. Our results demonstrate the potential evolutionary dynamics of a plastidic region generally regarded as highly conserved and probably cotranscribed and, as shown here for several genera among cruciferous plants, greatly characterized by parallel gains and losses of duplicated trnF copies.