\u3cem\u3eDispora Speciosa\u3c/em\u3e, A New Addition to the Genus \u3cem\u3eParallela\u3c/em\u3e and the First Coccoid Member of the Family Microsporaceae

The clade that currently represents the green algal family Microsporaceae is one of the few filament-forming groups of Chlorophyceae. Molecular phylogenies show this clade containing the genus Microspora and the more recently circumscribed Parallela, whose filaments are loosely arranged and often multiseriate. We initially investigated the enigmatic bog-loving Dispora speciosa as a commonly accepted member of the mucilage-forming Radiococcaceae or a putative member of crucigenoid chlorophytes (a non-monophyletic group formerly placed in Scenedesmaceae) based on its two-dimensional colony formation. However, our plastid and nuclear ribosomal phylogenies confidently placed Dispora within the genus Parallela instead, and therefore distantly related to both Radiococcaceae and crucigenoids. Upon further examination of the cell morphology and ultrastructure, we found several corresponding features between Dispora and Parallela, despite Dispora’s apparent coccoid-colonial gross morphology. Both genera have cells with a parietal plastid positioned around a large central nucleus. The loose, multiseriate filament formation in Parallela can be interpreted as similar to Dispora’s flat colony formation in its natural state. Because we only present data from one non-type species and strain of Dispora, we cannot merge the entire genus with Parallela. We do however argue that D. speciosa, of which this strain is the sole available, morphologically and ecologically faithful representative, should be transferred into Parallela, and the specimen prepared from strain ACOI 1508 be designated as type. Our study also impacts the current view on evolution of multicellular (colonial and filamentous) forms in Chlorophyceae

Genome Sequence of \u3cem\u3eBacillus\u3c/em\u3e Phage Saddex

The complete genome of Bacillus phage Saddex was determined and annotated in this study. Saddex has distinct sections with similarities to other Bacillus phages, such as Kida, even though these phages were isolated more than 800 km apart by separate laboratories

Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta)

The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta). We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in “Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution” (Fučíková et al., In review) [1]

Annotation guidelines for German verbal synonyms included in SynSemClass Lexicon

This report presents a guideline for including German synonyms into the multilingual SynSemClass lexicon

Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations

Spatial variation in disease risk in wild populations can depend both on environmental and genetic factors. Understanding the various contributions of each factor requires experimental manipulation of both the environment and genetic composition of populations under natural field conditions. We first examined natural patterns of oomycete composition and infection in the eggs of 13 populations of the spotted salamander Ambystoma maculatum. We then performed a fully factorial field transplant of the eggs of six populations to separate the contributions from population of origin and the environment on oomycete resistance in spotted salamanders. Among wild ponds, we found strong variation in oomycete infections in spotted salamander populations and differences in the composition of oomycete communities. In transplant experiments, salamander populations differed in their resistance to oomycete infections via a significant interaction between population of origin and environment. However, not all populations were locally adapted to local conditions. One population was significantly adapted to its home environment, and another one was significantly maladapted. These population effects could originate from differential adaptation of salamander populations to local oomycete communities or environmental conditions that mediate resistance, local adaptation and maladaptation of oomycetes to hosts, or from maternal transmission. Accounting for both environment and population of origin will often be necessary to understand disease dynamics in wild populations

Dryad

Data matrices and scripts to repeat all analyses presented in the paper

SynSemClass 3.5

The SynSemClass synonym verb lexicon version 3.5 investigates, with respect to contextually-based verb synonymy, semantic ‘equivalence’ of Czech, English and German verb senses and their valency behavior in parallel Czech-English and German-English language resources. SynSemClass3.5 is a multilingual event-type ontology based on classes of synonymous verb senses, complemented with semantic roles and links to existing semantic lexicons. Apart of the already used links to PDT-Vallex, EngVallex, CzEngVallex, FrameNet, VerbNet, PropBank, Ontonotes, and English WordNet for Czech and English entries the new links to German language lexical resources are exploited for German verb entries, such as Woxikon, E-VALBU, and GUP. The German part of the lexicon has been created within the project Multilingual Event-Type-Anchored Ontology for Natural Language Understanding (META-O-NLU) by two cooperating teams - by the team of the Charles University, Faculty of Mathematics and Physics, Institute of Formal and Applied Linguistics, Prague (ÚFAL), Czech Republic and the team of the German Research Center for Artificial Intelligence (DFKI) Speech and Language Technology, Berlin, Germany

Making a Semantic Event-type Ontology Multilingual

We present an extension of the SynSemClass event-type ontology, originally conceived as a bilingual Czech-English resource. We added German entries to the classes representing the concepts of the ontology. Having a different starting point than the original work (unannotated parallel corpus without links to a valency lexicon and, of course, different existing lexical resources), it was a challenge to adapt the annotation guidelines, the data model and the tools used for the original version. We describe the process and results of working in such a setup. We also show the next steps to adapt the annotation process, data structures and formats and tools necessary to make the addition of a new language in the future more smooth and efficient, and possibly to allow for various teams to work on SynSemClass extensions to many languages concurrently. We also present the latest release which contains the results of adding German, freely available for download as well as for online access

Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using Next-Generation sequencing methods. Plastomes were characterized and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. Key results: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. Conclusions: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex