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Fig. 7 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 7. Representative photographs of slides with Lyperosomum tenori sp. n. (upper part of the figure) and Lyperosomum hirundinis sp. n. (lower part of the figure). Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic. Photographs of L. hirundinis sp. n. are composite photographs merged from multiple images. Note that the seeming differences in forebody shape of L. tenori sp. n. individuals is caused by differences in handling with host birds prior the fixation of the trematodes - L. tenori sp. n. from hosts that were frozen prior the examination are highly susceptible to forebody prolongation.

Fig. 11 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 11. Representative photographs of slides with Stromitrema acrocephali sp. n. and Lutztrema atricapillae. Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic.

Fig. 6 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 6. Drawings of holotype specimens of Lyperosomum tenori sp. n. (A), Lyperosomum atricapillae sp. n. (B), Stromitrema acrocephali sp. n. (C), Lutztrema atricapillae sp. n. (D), and Lyperosomum hirundinis sp. n. (E–F).

Fig. 8 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 8. Representative photographs of slides with Lyperosomum atricapillae sp. n. Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic.

Fig. 4. A in Life history strategies of Cotylurus spp. Szidat, 1928 (Trematoda, Strigeidae) in the molecular era - Evolutionary consequences and implications for taxonomy

Fig. 4. A median-joining network of COI haplotype of Cotylurus. Each circle represents a unique haplotype where the diameter is proportional to the number of DNA sequences represented.

Fig. 1 in Life history strategies of Cotylurus spp. Szidat, 1928 (Trematoda, Strigeidae) in the molecular era - Evolutionary consequences and implications for taxonomy

Fig. 1. The phylogenetic relationships within genus Cotylurus based on the concatenated COI mtDNA and 28S rDNA markers. The analysis was performed by the use of Bayesian inference, diamond symbol indicates posterior probability greater than 90%.

Fig. 3 in Life history strategies of Cotylurus spp. Szidat, 1928 (Trematoda, Strigeidae) in the molecular era - Evolutionary consequences and implications for taxonomy

Fig. 3. The phylogenetic relationships within the genus Cotylurus based on COI mtDNA marker. The analysis was performed by the use of Bayesian inference, diamond symbol indicates posterior probability greater than 90%.

Fig. 2 in Life history strategies of Cotylurus spp. Szidat, 1928 (Trematoda, Strigeidae) in the molecular era - Evolutionary consequences and implications for taxonomy

Fig. 2. The phylogenetic relationships within the genus Cotylurus based on 28S rDNA marker. The analysis was performed by the use of Bayesian inference, diamond symbol indicates posterior probability greater than 90%.

opencc-by-4.0Jan 2024View details →

The North Pacific Eukaryotic Gene Catalog: metatranscriptome assemblies with taxonomy, function and abundance annotations

This data continues with the development of the unprocessed NPEGC Trinity de novo metatranscriptome assemblies, uploaded to this Zenodo repository for raw assemblies: <a href="../records/7332796">The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3</a> A full description of this data is published in Scientific Data, available here: <a href="https://www.nature.com/articles/s41597-024-04005-5" target="_blank" rel="noopener">The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations</a>. Please cite this publication if your research uses this data: Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161. Excerpts of key processing steps are sampled below with links to the detailed code on the main github code repository: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog">https://github.com/armbrustlab/NPac_euk_gene_catalog</a> Processing and annotation of protein-level NPEGC metatranscripts is done in 6 primary steps: 1. Six-frame translation into protein sequences 2. Frame-selection of protein-coding translation frames 3. Clustering of protein sequences at 99% sequence identity 4. Taxonomic annotation against MarFERReT v1.1 + MARMICRODB v1.0 multi-kingdom marine reference protein sequence library with DIAMOND 5. Functional annotation against Pfam 35.0 protein family HMM profiles using HMMER3 6. Functional annotation against KOfam HMM profiles (KEGG release 104.0) using KofamScan v1.3.0 <code># Define local NPEGC base directory here:</code> <code>NPEGC_DIR="/mnt/nfs/projects/armbrust-metat"</code> <code># Raw assemblies are located in the /assemblies/raw/ directory</code> <code># for each of the metatranscriptome projects</code> <code>PROJECT_LIST="D1PA G1PA G2PA G3PA G3PA_diel"</code> <code># raw Trinity assemblies:</code> <code>RAW_ASSEMBLY_DIR="${NPEGC_DIR}/${PROJECT}/assemblies/raw"</code> Translation We began processing the raw metatranscriptome assemblies by six-frame translation from nucleotide transcripts into three forward and three reverse reading frame translations, using the transeq function in the EMBOSS package. We add a cruise and sample prefix to the sequence IDs to ensure unique identification downstream (ex, `>TRINITY_DN2064353_c0_g1_i1_1`  to `>G1PA_S09C1_3um_TRINITY_DN2064353_c0_g1_i1_1` for the S09C1_3um sample in the G1PA assemblies). See <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.6tr_frame_selection_clustering.sh">NPEGC.6tr_frame_selection_clustering.sh</a> for full code description. Example of six-frame translation using transeq <code>transeq -auto -sformat pearson -frame 6 -sequence 6tr/${PREFIX}.Trinity.fasta -outseq 6tr/${PREFIX}.Trinity.6tr.fasta</code> Frame selection We use a custom frame-selection python script <a href="https://github.com/armbrustlab/marferret/blob/main/scripts/python/keep_longest_frame.py">keep_longest_frame.py</a> to determine the longest coding length in each open reading frame and retain this sequence (or multiple sequences if there is a tie) for downstream analyses.  See <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.6tr_frame_selection_clustering.sh">NPEGC.6tr_frame_selection_clustering.sh</a> for full code description. Clustering by sequence identity To reduce sequence redundancy and near-identical sequences, we cluster protein sequences at the 99% sequence identity level and retain the sequence cluster representative in a reduced-size FASTA output file. See <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.6tr_frame_selection_clustering.sh">NPEGC.6tr_frame_selection_clustering.sh</a> for full code description of linclust/mmseqs clustering. Sample of linclust clustering script: core mmseqs function <code>function NPEGC_linclust {</code> <code># make an index of the fasta file:</code> <code>$MMSEQS_DIR/mmseqs createdb $FASTA_PATH/$FASTA_FILE NPac.$STUDY.bf100.db</code> <code># cluster sequences at $MIN_SEQ_ID</code> <code>$MMSEQS_DIR/mmseqs linclust NPac.${STUDY}.bf100.db NPac.${STUDY}.clusters.db NPac_tmp --min-seq-id ${MIN_SEQ_ID}</code> <code># retieve cluster representatives:</code> <code>$MMSEQS_DIR/mmseqs result2repseq NPac.${STUDY}.bf100.db NPac.${STUDY}.clusters.db NPac.${STUDY}.clusters.rep</code> <code># generate flat FASTA output with cluster reps</code> <code>$MMSEQS_DIR/mmseqs result2flat NPac.${STUDY}.bf100.db NPac.${STUDY}.bf100.db NPac.${STUDY}.clusters.rep NPac.${STUDY}.bf100.id99.fasta --use-fasta-header</code> <code>}</code> Corresponding files uploaded to this repository: Gzip-compressed FASTA files after translation, frame-selection, and clustering at 99% sequence identity (.bf100.id99.aa.fasta.gz)     NPac.G1PA.bf100.id99.aa.fasta.gz     NPac.G2PA.bf100.id99.aa.fasta.gz     NPac.G3PA.bf100.id99.aa.fasta.gz     NPac.G3PA_diel.bf100.id99.aa.fasta.gz     NPac.D1PA.bf100.id99.aa.fasta.gz MarFERReT + MARMICRODB taxonomic annotation with DIAMOND Taxonomy was inferred for the NPEGC metatranscripts with the DIAMOND fast read alignment software against the <a href="../records/10586950">MarFERReT v1.1 + MARMICRODB v1.0 multi-kingdom marine reference protein sequence library (v1.1)</a>, a combined database of the <a href="https://doi.org/10.1038/s41597-023-02842-4">MarFERReT v1.1 marine microbial eukaryote sequence library</a> and <a href="https://doi.org/10.5281/zenodo.3520509">MARMICRODB v1.0 </a>prokaryote-focused marine genome database. See <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.diamond_taxonomy.log.sh">NPEGC.diamond_taxonomy.log.sh</a> for full description of DIAMOND annotation. Excerpt of core DIAMOND function: <code>function NPEGC_diamond {</code> <code># FASTA filename for $STUDY</code> <code>FASTER_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"</code> <code># Output filename for LCA results in lca.tab file:</code> <code>LCA_TAB="NPac.${STUDY}.MarFERReT_v1.1_MMDB.lca.tab"</code> <code>echo "Beginning ${STUDY}"</code> <code>singularity exec --no-home --bind ${DATA_DIR} \</code> <code>        "${CONTAINER_DIR}/diamond.sif" diamond blastp \</code> <code>        -c 4 --threads $N_THREADS \</code> <code>        --db $MFT_MMDB_DMND_DB -e $EVALUE --top 10 -f 102 \</code> <code>        --memory-limit 110 \</code> <code>        --query ${FASTER_FASTA} -o ${LCA_TAB} >> "${STUDY}.MarFERReT_v1.1_MMDB.log" 2>&1</code> <code>}</code> Corresponding files uploaded to this repository: Gzip-compressed diamond lowest common ancestor predictions with NCBI Taxonomy against a combined MarFERReT + MARMICRODB taxonomic library (*.Pfam35.domtblout.tab.gz)     NPac.G1PA.MarFERReT_v1.1_MMDB.lca.tab.gz     NPac.G2PA.MarFERReT_v1.1_MMDB.lca.tab.gz     NPac.G3PA.MarFERReT_v1.1_MMDB.lca.tab.gz     NPac.G3PA_diel.MarFERReT_v1.1_MMDB.lca.tab.gz     NPac.D1PA.MarFERReT_v1.1_MMDB.lca.tab.gz Pfam 35.0 functional annotation using HMMER3 Clustered protein sequences were annotated against the Pfam 35.0 collection of 19,179 protein family Hidden Markov Models (HMMs) using <a href="http://hmmer.org/">HMMER 3.3 </a> with the <a href="https://academic.oup.com/nar/article/49/D1/D412/5943818">Pfam 35.0 protein family database</a>. Pfam annotation code is documented here: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.hmmer_function.sh">NPEGC.hmmer_function.sh</a> Excerpt of core hmmsearch function: <code>function NPEGC_hmmer {</code> <code># Define input FASTA</code> <code>INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"</code> <code># hmmsearch call:</code> <code>hmmsearch --cut_tc --cpu $NCORES --domtblout $ANNOTATION_DIR/${STUDY}.Pfam35.domtblout.tab $HMM_PROFILE ${INPUT_FASTA}</code> <code># compress output file:</code> <code>gzip $ANNOTATION_DIR/${STUDY}.Pfam35.domtblout.tab</code> <code>}</code> Corresponding files uploaded to this repository: Gzip-compressed hmmsearch domain table files for Pfam35 queries (*.Pfam35.domtblout.tab.gz)     G1PA.Pfam35.domtblout.tab.gz     G2PA.Pfam35.domtblout.tab.gz     G3PA.Pfam35.domtblout.tab.gz     G3PA_diel.Pfam35.domtblout.tab.gz     D1PA.Pfam35.domtblout.tab.gz KEGG functional annotation using KofamScan v1.3.0 Clustered protein sequences were annotated against the KEGG collection (release 104.0) of 20,819 protein family Hidden Markov Models (HMMs) using <a href="https://github.com/takaram/kofam_scan" target="_blank" rel="noopener">KofamScan </a>and KofamKOALA. Kofam annotation code is documented here: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.kofamscan_function.sh">NPEGC.kofamscan_function.sh</a> Excerpt of core NPEGC_kofam function: <code># Core function to perform KofamScan annotation</code> <code>function NPEGC_kofam {</code> <code>    # Define input FASTA</code> <code>    local INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"</code> <code>    # KofamScan call</code> <code>    ${KOFAM_DIR}/kofam_scan-1.3.0/exec_annotation -f detail-tsv -E ${EVALUE} -o ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv ${FASTA_DIR}/${INPUT_FASTA}</code> <code>    # Keep best hit (data is already sorted by KofamScan)</code> <code>    sort -uk1,1 ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv > ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.best.kofam.tsv</code> <code>    # Compress output file</code> <code>    gzip ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv</code> <code>    # Compress best.kofam output file</code> <code>    gzip ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.best.kofam.tsv</code> <code>}</code> <code># filter hits with a score > 30 in R</code> Corresponding files uploaded to this repository: Gzip-compressed KofamScan domain table files for Kofam queries (*.best.Kofam.incT30.csv.gz):     NPac.G1PA.bf100.id99.aa.best.Kofam.incT30.csv.gz     NPac.G2PA.bf100.id99.aa.best.Kofam.incT30.csv.gz     NPac.G3PA.UW.bf100.id99.aa.best.Kofam.incT30.csv.gz     NPac.G3PA.diel.bf100.id99.aa.best.kofam.incT30.csv.gz     NPac.D1PA.diel.bf100.id99.aa.best.kofam.incT30.csv.gz The full kofamscan tables with score >30 are deposited here: <a title="The North Pacific Eukaryotic Gene Catalog: KOfam protein function annotations" href="../records/13743267" target="_blank" rel="noopener">https://zenodo.org/records/13743267</a>

FIGURE 2 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 2. Scanning electron micrographs of the foraminifera specimens. Scale bar equals 100 µm. 1-3- Three different specimens of Polysaccammina ipohalina Scott, 1976b, illustrating the differences in size and form. In all specimens it is possible to see attached organic matter; 4-5- Polysaccammina hyperhalina Medioli, Scott, and Petrucci, 1983. 4- complete specimen of P. hyperhalina; 5- aperture view; 6- specimen with several side branches; 7-10- different sized specimens of Ammovertellina sp.; 11-14- various specimens of Reophax nana Rhumbler, 1913; 15-17- Leptohalysis scottii (Chaster, 1892); 15 and 16- side view of two complete specimens; 17- detail on the agglutination of the last chamber; 18- complete specimen of Ammobaculites exiguus Cushman and Brönnimann, 1948b; 19- Ammobaculites sp. with the uncoiled portion broken; 20-22- Ammotium salsum (Cushman and Brönnimann, 1948a); 20- best specimen; 21- smaller specimen; 22- aperture detail; 23- Ammotium sp.; 24-26- different specimens of Miliammina fusca (Brady, 1870); 27-28- Miliammina obliqua Heron-Allen and Earland, 1930; 27- view of the interio-marginal arch of the aperture; 29-30- Arenoparrella mexicana (Kornfeld, 1931); 29- ventral side with view to main aperture and supplementary apertures; 30- dorsal side with view to supplementary apertures; 31-32- Deuterammina eddystonensis Brönnimann and Whittaker, 1990; 31- dorsal view; 32- ventral view; 33-35- Jadammina macrescens (Brady, 1870); 33- dorsal view; 34- ventral view; 35- dorsal view of a deformed test.

FIGURE 1 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 1. Location of the study area; 1) Geographical context of the Guadiana River basin in the Iberian Peninsula (Europe). Adapted from chguadiana.es (2012). Coordinate system: Datum ETRS89 UTM Zone 30N; 2) Study area: Map of the Guadiana Estuary with site locations.

FIGURE 7 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 7. Distribution patterns of the common to dominant species in the samples collected in winter along a distance-to-sea and elevation gradients (in relation to MSL).

FIGURE 4 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 4. Scanning electron micrographs of the foraminifera specimens. Scale bar equals 100 µm. 1-4- different sized specimens of Bolivina ordinaria Phleger and Parker, 1952, new name; 5- Buliminella elegantissima (d'Orbigny, 1839b); 6-7- Cornuspira involvens (Reuss 1850); 8-10- Miliolid sp1; 8- apertural view; 9- front view; 10- back view; 11- 13- Miliolid sp2; 11- apertural view; 12- front view; 13- back view; 14-16- Miliolid sp3; 14- front view; 15- apertural view; 16- back view; 17-18- Miliolid sp4; 17- apertural view; 18- front view; 19-21- Miliolid sp5; 19- apertural view; 20- front view; 21- back view; 22-23- Miliolid sp6; 22- front and apertural view; 23- back view; 24-26- Miliolid sp7; 24- front view; 25- apertural view; 26- front and apertural view; 27-29- Miliolid sp8; 27- front view; 28- apertural view; 29- front view of a smaller specimen.

FIGURE 8 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 8. Distribution patterns of the common to dominant species in the samples collected in summer along a distance-to-sea and elevation gradients (in relation to MSL).

FIGURE 3 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 3. Scanning electron and light microscope micrographs of the foraminifera specimens. Scale bar equals 100 µm except where noted otherwhise; 1-2- Jadammina macrescens (Brady, 1870); 1- supplementary apertures view; 2- detail of supplementary apertures (scale bar = 50 µm); 3-4- Lepidodeuterammina plymouthensis Brönnimann and Whittaker, 1990; 3- dorsal view; 4- ventral view; 5-8- Lepidodeuterammina ochracea (Williamson, 1858); 5- dorsal view; 6- ventral view; 7- dorsal view of a smaller specimen; 8- ventral view of a smaller specimen; 9-10- Portatrochammina sp.; 9- dorsal view; 10- ventral view; 11-13- Siphotrochammina sp.; 11- dorsal side with inter-cameral foramen view; 12- dorsal view of a smaller specimen, also with inter-cameral foramen; 13- ventral view of a smaller specimen; 14-16- Tiphotrocha comprimata Saunders, 1957; 14- dorsal view; 15- ventral view; 16- individual strongly attached to a sea-grass leaf; detail of a Pinus pollen grain at the center of the leaf; 17-21- Trochammina inflata (Montagu, 1808); 17- dorsal view; 18- ventral view; 19- ventral view with umbilical tube detail; 20- microspheric form dorsal view; 21- microspheric form ventral view; 22- Eggerelloides scaber (Williamson, 1858); 23-25- Textularia earlandi Parker, 1952; 23- apertural view; 24- lateral view; 25- profile view with aperture in detail; 26-29- Discorinopsis aguayoi (Bermúdez, 1935); 26- scanning electron dorsal view; 27- scanning electron ventral view; 28- light microscope dorsal view; 29- light microscope ventral view.

FIGURE 6 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 6. RDA attribute plot representing the distribution and abundance of the dominant species in Guadiana Estuary according to elevation and distance-to-sea variables.

FIGURE 5 in Taxonomy, ecology and biogeographical trends of dominant benthic foraminifera species from an Atlantic-Mediterranean estuary (the Guadiana, southeast Portugal)

FIGURE 5. Scanning electron and light microscope micrographs of the foraminifera specimens. Scale bar equals 100 µm. 1- Lamarckina haliotidea (Heron-Allen and Earland, 1911) ventral view; 2-3- Asterigerinata mamilla (Williamson, 1858); 2- dorsal view; 3- ventral view; 4-5- Discorbis sp.; 4- dorsal view; 5- ventral view; 6-7- Helenina anderseni (Warren, 1957); 6- dorsal view; 7- ventral view; 8- Haynesina depressula (Walker and Jacob, 1798) side view; 9- Haynesina germanica (Ehrenberg, 1840) side view; 10- Elphidium advenum (Cushman, 1922) side view; 11- Elphidium excavatum (Terquem, 1875) side view; 12-15- Elphidium wiliamsoni Haynes, 1973; 12- side view in light microscope image; 13- side view in scanning electron image; 14- profile view in scanning electron image; 15- side view of a smaller specimen in scanning electron image; 16-18- side view of different size Elphidium gerthi Van Voorthuysen, 1957; 19-21- Elphidium oceanensis (d'Orbigny, 1826); 19- side view in scanning electron image; 20- profile view in scanning electron image; 21- side view in light microscope image; 22- Elphidium poeyanum (d'Orbigny, 1826) side view; 24-27- Ammonia sp1; 24- dorsal view; 25- profile view; 26- ventral view; 27- dorsal view in light microscope image; 28-31- Ammonia sp2 (Ammonia aberdoveyensis Haynes, 1973); 28- dorsal view; 29- profile view; 30- ventral view; 31- dorsal view in light microscope image; 32-35- Ammonia sp3 (Ammonia aberdoveyensis Haynes, 1973); 32- dorsal view; 33- profile view; 34- ventral view; 35- dorsal view in light microscope image.

opencc-by-4.0Oct 2015View details →

Fig. 4 in Short Communication On the distribution, taxonomy, and natural history of the Indian Smooth Snake, Coronella brachyura (Günther, 1866)

Fig. 4. Map showing distribution range of Coronella brachyura (For all the localities: 1–13, reference Table 2).

opencc-by-4.0Oct 2015View details →

Fig. 2 in Short Communication On the distribution, taxonomy, and natural history of the Indian Smooth Snake, Coronella brachyura (Günther, 1866)

Fig. 2. Lateral aspect of Coronella brachyura (NCS 2); a, left side showing 8 supralabials and 5th supralabial partly divided; b, right side showing 9 supralabials, 4–6th touching eye.