New insight into the taxonomy of Cephaloziellaceae (Marchantiophyta): the family of the smallest higher plants on Earth.

An analysis of the phylogeny of Cephaloziellaceae was carried out based on trees constructed for previously and newly obtained sequences of five genes: nuclear ITS1-2 and chloroplast trnL-F, trnG, rbcL, and psbA. Phylogenetic trees inferred from different genes are congruent for the main details; however, the position of several taxa is variable. As a result, a new phylogenetic system of the family was proposed. The narrow genus concept seems to be more appropriate for the family. Cephaloziella spinicaulis is segregated into the new genus Douiniella, the generic status for Prionolobus and Metacephalozia is confirmed, and the dubious generic status of Kymatocalyx is substantiated. The generic independence of Cylindrocolea from Cephaloziella s. str. is confirmed. The small amount of data hinders the description of two more genera from Cephaloziella s.l.

The Position of Lophozia dubia (Lophoziaceae, Marchantiophyta) in the Phylogenetic System of Lophozia and the Distribution of Lophozia in Southeast Eurasia, Extending to Indonesia.

Lophozia pallida, the commonly used name for a rare and little-known Sino-Himalayan species, was found to be a synonym of Lophozia dubia, a forgotten and previously misinterpreted species known in Indonesia. A comparative study of herbarium materials and our collections made it possible to 'extend' the distribution of Lophozia s. str. southward to Indonesia. The description of oil bodies from the species is provided for the first time. The position of the species in the Lophozia phylogenetic system demonstrates its clear differences from the morphologically similar Lophozia guttulata and its phylogenetic relationship with the Japanese-Korean Lophozia koreana.

Calypogeia (Calypogeiaceae, Marchantiophyta) in Pacific Asia: Updates from Molecular Revision with Particular Attention to the Genus in North Indochina.

Calypogeia is a genus in Pacific Asia that is difficult to classify taxonomically. These difficulties arise from (1) considering the presence of oil bodies as anatomical characters for taxonomic differentiation, (2) the wide occurrence of sibling, semicryptic and geographical vicariant taxa and (3) the inevitable need to organize new datasets for molecular genetic revision of the genus. The present study uses an integrative approach, including molecular genetic, morphological, chorological and ecological methods, to understand the taxonomy of the genus in Amphi-Pacific Asia. As a result, a set of new-to-science taxa was revealed, and the suite of morphological features necessary for reliable discrimination of the taxa was revised. These results are based on the study of a large set of 'fresh' collections suitable for molecular analysis and morphological comparison and include data on oil bodies. The most basal branch in Calypogeia s.l. is segregated into a new genus, Asperifolia. Descriptions of the new taxa and the key to Calypogeia in Vietnam are provided.

The systematic position of puzzling Sino-Himalayan Lophocoleasikkimensis (Lophocoleaceae, Marchantiophyta) is identified.

Lophocoleasikkimensis, a little-known Sino-Himalayan species, was collected in North Vietnam and its taxonomic position was identified by molecular genetic techniques. The species is characterized by generally narrowly pointed leaves, which are not seen in other representatives of Lophocoleaceae. We found that it belongs to the recently described genus Cryptolophocolea, although it is clearly morphologically dissimilar to other members of the genus. We propose a corresponding nomenclature combination: Cryptolophocoleasikkimensis comb. nov. This species is the only one in its genus with a predominantly Sino-Himalayan distribution; the vast majority of congeners are distributed in the Southern Hemisphere (mostly in Australasia). Reports of this species in Vietnam further confirm the close phytogeographic relationships of the flora of northern Indochina with those of the Sino-Himalayas and suggest that this species is found in other parts of the Hoang Lien Range and the southern Hengduan Range.

Seasonal Variability of Photosynthetic Microbial Eukaryotes (<3 µm) in the Kara Sea Revealed by 18S rDNA Metabarcoding of Sediment Trap Fluxes.

This survey is the first to explore the seasonal cycle of microbial eukaryote diversity (<3 µm) using the NGS method and a 10-month sediment trap (2018-2019). The long-term trap was deployed from September to June in the northwestern part of the Kara Sea. A water sample collected before the sediment trap was deployed and also analyzed. The taxonomic composition of microbial eukaryotes in the water sample significantly differed from sediment trap samples, characterized by a high abundance of Ciliophora reads and low abundance of Fungi while trap samples contained an order of magnitude less Ciliophora sequences and high contribution of Fungi. Photosynthetic eukaryotes (PEs) accounting for about 34% of total protists reads were assigned to five major divisions: Chlorophyta, Cryptophyta, Dinoflagellata, Haptophyta, and Ochrophyta. The domination of phototrophic algae was revealed in late autumn. Mamiellophyceae and Trebouxiophyceae were the predominant PEs in mostly all of the studied seasons. Micromonas polaris was constantly present throughout the September-June period in the PE community. The obtained results determine the seasonal dynamics of picoplankton in order to improve our understanding of their role in polar ecosystems.

The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters.

Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To gain more knowledge about Mamiellophyceae distribution and diversity special studies were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July-September 2017 in the Barents, Kara and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A-uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with Micromonas polaris dominating north of 72°N. The presence of Ostreococcus tauri, Ostreococcus lucimarinus and Ostreococcus mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.

Overview of Schistochilopsis (Hepaticae) in Pacific Asia with the Description Protochilopsis gen. nov.

The taxonomic diversity center of Schistochilopsis is in East Asia, where the genus also shows the highest genetic diversity and morphological plasticity. The integrative survey of Schistochilopsis in East Asia was the main goal of the present account. Plant materials were obtained from recent collections made by authors in various parts of amphi-Pacific Asia; several types of specimens were also studied. The study includes phylogenetic reconstructions from nuclear ITS1,2, chloroplast trnL and trnG sequences, and anatomo-morphological, biogeographical, and taxonomical analyses. As a result, it was concluded that S. obscura should be transferred to Lophozia s. str. and S. grandiretis to the newly described genus Protochilopsis. Lophozia boliviensis was found to be part of the Andean-Sino-Himalayan taxon belonging to Schistochilopsis. The species status of S. hyperarctica and S. opacifolia was not confirmed. Substantial genetic variation is observed within S. incisa with possible cryptic sympatric distributed entities. The taxonomical section of the paper provides a discussion on the status, distinctive morphological traits, distribution, and ecology supplemented with the morphological description for poorly understood taxa. In the vast majority of cases, the illustrations and photographs made from the types and living material are provided.

Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.

Operational taxonomic units 94%-95% similar to the known Pedinophyceae were found as a result of high-through sequencing of 18S rDNA V4 amplicons of environmental DNA from the summer picophytoplankton samples from the White Sea. Partial sequence of a ribosomal operon (the 5,298 bp includes partial 18S and 28S rDNA, complete 5.8S rDNA, ITS1, and ITS2 sequences) and a partial 2,112 bp chloroplast 23S rDNA sequence White Sea Pedinophyceae was amplified from metagenomic DNA by specific primers and sequenced. A new phylotype was designated as uncultured Pedinophyceae WS. On Chlorophyta phylogenetic trees the discovered phylotype occupies a basal position in the Marsupiomonadales clade. The synapomorphic base substitutions in rRNA hairpins confirm the relationship of Pedinophyceae WS to Marsupiomonadales and its difference from known genera of the order. The obtained results extend knowledge of picophytoplankton diversity in subarctic waters.

Correction: Complete mitochondrial genome sequence of the "copper moss" Mielichhoferia elongata reveals independent nad7 gene functionality loss.

[This corrects the article DOI: 10.7717/peerj.4350.].

Complete mitochondrial genome sequence of the "copper moss" Mielichhoferia elongata reveals independent nad7 gene functionality loss.

The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages. Evaluation of the microsatellite (simple sequence repeat) content of the M. elongata mitochondrial genome indicates that it could be used as a tool in further studies as a phylogenetic marker. The strongly supported phylogenetic tree presented here, derived from 33 protein coding sequences of 40 bryophyte species, is consistent with other reconstructions based on a number of different data sets.

Phylogeny and systematics of the genus Lophozia s. str. (Dumort.) Dumort. (Hepaticae) and related taxa from nuclear ITS1-2 and chloroplast trnL-F sequences.

Nuclear ITS1-2 and chloroplast trnL-F were sequenced for 21 taxa of Lophozia s. str., two species of Protolophozia, five species of Schistochilopsis, three species of Barbilophozia and Obtusifolium obtusum. The topologies of phylogenetic trees for 49 taxa constructed from combined sequences of these regions by maximum parsimony, maximum likelihood and Bayesian methods are similar. The species of Lophozia s. str., excluding Lophozia sudetica, combine into two main clades and these contradict subdivisions of Lophozia s. str. based on morphology. The species status of Lophozia lantratoviae is confirmed, whereas Lophozia austro-sibirica is almost identical to Lophozia ventricosa var. guttulata. The genus Schistochilopsis is paraphyletic and occupies basal position to Lophozia s. str., while O. obtusum is clearly separated from Schistochilopsis. A low level of divergence was found between L. sudetica and Protolophozia debiliformes, which are closer to Barbilophozia than to Lophozia s. str. Molecular divergence between geographically remote populations of L. sudetica, Lophozia silvicoloides and Protolophozia debiliformis are low as opposed to those of Lophozia polaris, Lophozia pellucida or Lophozia excisa. Consideration of the trnL intron P8 region indels alone can adequately assign some clades revealed by tree building. A consensus secondary structure of the trnL intron P8 region could not be inferred for taxa studied mainly due to high sequence length diversity originated from deletions.