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TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
Data from: ITS all right mama: Investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: Perseus and UCHIME. Large proportions of the chimeras reported were false positives. No false negatives were found in the dataset. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric "parent sequences" had significantly higher percent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighboring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seem to buffer the rate of chimera formation in comparison to other, less variable barcoding regions, due to shorter regions of high sequence similarity.
Chimeric Origin of Eukaryotes from Asgard archaea and Giant viruses
<p>This repository contains supplementary data for the study "Chimeric Origin of Eukaryotes from Asgard archaea and Giant viruses"</p>
Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14, BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE, BM chimeric mice (CD45.2 <em>Csf2rb</em><sup>-/-</sup>: CD45.1 <em>Csf2rb</em><sup>+/+</sup> and CD45.2 <em>Ifngr1<sup>-/-</sup></em>: CD45.1 <em>Ifngr1<sup>+/+</sup></em>) using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
Chimeric inheritance and crown-group acquisitions of Carbon fixation genes within Chlorobiales
<p class="MsoNormal">The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to ~1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.<span> </span></p>
Fig. 2 in The puzzling taxonomic rank of Pijnackeria hispanica, a chimerical hybrid androgen (Insecta, Phasmida)
Fig. 2 Ranges of Pijnackeria taxa. 2n: A, P. lucianae; B, P. barbarae; C, P. lelongi; D, P. originis; 3n, P. masettii; 4n, P. hispanica. Sample acronyms as in Ghiselli et al. (2007). The area of P. recondita (Sierra Nevada) and P. hispanica (El Purche) samples is represented by a single dot south-east of PRA (Puerto La Ragua). Acronyms as in Tables 1 and 2
Fig. 5 in The puzzling taxonomic rank of Pijnackeria hispanica, a chimerical hybrid androgen (Insecta, Phasmida)
Fig. 5 Karyotype of Pijnackeria recondita. The karyotype is very similar to those of all other Pijnackeria species. a Female: 1st pair, heterochromosomes; the 2nd and 4th pairs bear a heterozygous satellite; b male: its unique sex chromosome (X0) allows indicating the first female pair as the heterochromosome pair in both P. recondita and, as a consequence, in P. hispanica
Fig. 3 in The puzzling taxonomic rank of Pijnackeria hispanica, a chimerical hybrid androgen (Insecta, Phasmida)
Fig. 3 Pijnackeria recondita food plants: Cytisus scoparius on the right and Cytisus sp. on the left
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
Chemical initial and boundary conditions for WRF-CHIMERE
<p>Chemical initial and boundary conditions for WRF-CHIMERE in eastern China during 2017.</p>
Supplementary Figure Legend S1: An overview of DNA samples included in the NGS based chimerism validation process and AlloSeq HCT library preparation workflow.
<p><strong>Supplementary Figure </strong><strong>Legend S1: </strong>An overview of DNA samples included in the NGS based chimerism validation process and AlloSeq HCT library preparation workflow. <strong>S1a: </strong>An overview of clinical and artificial DNA included in the NGS based chimerism validation process (Clinical samples, Artificial construct samples and ASHI EMO Proficiency samples). <strong>S1b:</strong> Schematic presentation of time required for the NGS Chimerism assay. <strong>S1c.</strong> AlloSeq HCT library preparation workflow.</p>
Figure 11 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 11. Secondary structure of the 18S rRNA molecule of Hysterocineta bellerophon. Arrows mark molecular synapomorphies of the 'paravorax' clade. Primary nucleotide homologies are scaưered throughout the whole 18S rRNA molecule, suggesting a long common evolution of the 'paravorax' clade. Thus, 'paravorax' clade-specific nucleotide characters are situated in terminal loops of helices (six nucleotide positions), bulges (six positions), single-stranded regions (four positions), and double-stranded regions (32 positions). There are as many as 48 molecular synapomorphies and four indels in the 18S rRNA molecule, corroborating the common origin of hysterocinetids and other members of the 'paravorax' clade. Mutations in the double-stranded regions are typically involved in compensatory base changes or retain helical structure when involved in non-canonical pairings in helices 27 and 43. The 18S secondary structure map of Saccharomyces cerevisiae (inset) is from hưp://apollo.chemistry.gatech.edu/RibosomeGallery.
Figure 8 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 8. Phylogenetic tree based on the nuclear 18S rRNA gene and mitochondrial COI sequences, showing the phylogenetic position of hysterocinetids within the subclass Hymenostomatia. Ichthyophthirius multifiliis was used as an outgroup, following Zhang and Vďačný (2022). Posterior probabilities for Bayesian inference conducted in MrBayes and bootstrap values for maximum likelihood conducted in IQ-Tree were mapped onto the 50%-majority rule Bayesian consensus tree. Fully statistically supported nodes are marked with red solid circles. The scale bar denotes two substitutions per 10 nucleotide positions. The oral apparatus of tetrahymenids is morphologically plastic (right inset). Most species have maintained the plesiomorphic condition, while some have completely lost the oral apparatus (Clausilocola) or have evolved a highly complex, peritrich-like oral ciliature that was displaced posteriorly (hysterocinetids). Diagrams of Tetrahymena and Clausilocola in the right inset are from Zhang and Vďačný (2022, 2023).
Figure 10 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 10. Phylogenetic tree based on the nuclear 18S and mitochondrial 16S rRNA gene sequences, showing the phylogenetic position of hysterocinetids within the class Oligohymenophorea. Note that hysterocinetids are nested within the 'paravorax' clade of the genus Tetrahymena. The 'paravorax' clade, at the present state of knowledge, comprises both free-living (e.g. T. paravorax), as well as endosymbiotic ciliates associated with freshwater planarians (T. nigricans), bivalves (T. glochidiophila and T. unionis), and lumbricid earthworms (Hysterocineta bellerophon and Protoptychostomum simplex). Posterior probabilities for Bayesian inference conducted in MrBayes and bootstrap values for maximum likelihood conducted in IQ-Tree were mapped onto the 50%-majority rule Bayesian consensus tree. Fully statistically supported nodes are marked with red solid circles. The scale bar denotes one substitution per ten nucleotide positions.
Figure 7 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 7. Phylogenetic tree based on the 18S rRNA gene, showing the phylogenetic position of hysterocinetids within the class Oligohymenophorea. The class Colpodea was used as an outgroup, following Zhang and Vďačný (2022). Although hysterocinetids are morphologically highly dissimilar from Tetrahymena, they are nested within its 'paravorax' clade with strong statistical support (100% ML bootstrap, 1.00 posterior probability). The 'paravorax' clade thus became paraphyletic and its name-bearing species T. paravorax is depicted as a sister-taxon of both hysterocinetids with full support. Posterior probabilities for Bayesian inference conducted in MrBayes and bootstrap values for maximum likelihood conducted in IQ-Tree were mapped onto the 50%-majority rule Bayesian consensus tree. Fully statistically supported nodes are marked with red solid circles. The scale bar denotes eight substitutions per 100 nucleotide positions.
Figure 14 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 14. Secondary structure of the C, 3ʹM and 3ʹm domains of the 16S rRNA molecule of Hysterocineta bellerophon. Arrows mark molecular synapomorphies of the 'paravorax' clade. Similarly to the homologous nuclear 18S, molecular synapomorphies are distributed across the whole 16S rRNA molecule: 13 nucleotides in the C domain, seven in the 3'M domain, and two in the 3'm domain. Thus, 'paravorax' cladespecific nucleotide characters are situated in terminal loops of helices (three nucleotide positions), bulges and single-stranded regions (seven positions), as well as in the double-stranded regions (12 positions). As in 18S and 28S, many more mutations are involved in Watson‒Crick and wobble pairings than in non-canonical interactions in the double-stranded regions of the 16S rRNA molecule. The 16S secondary structure map of Escherichia coli (inset) is from hưp://apollo.chemistry.gatech.edu/RibosomeGallery.
Figure 4 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 4. Hysterocineta bellerophon in vivo. A, D, less-side overviews, showing the variability of body shape and size, as well as of the nuclear apparatus. B, detail of the anterior body region, showing the dense somatic ciliature and the unciliated sucker. C, detail of the vacuolized oral area. E, detail of the posterior body region, showing the oral ciliature and the vacuolized cytoplasm. CV, contractile vacuole; FV, food vacuoles; IF, infundibulum; MA, macronucleus; OC, oral cilia; S, sucker; SC, somatic cilia. Scale bars = 20 µm (E), 30 µm (B), 50 µm (A), 100 µm (D).
Figure 2 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 2. Protoptychostomum simplex in vivo (A, B) and asser protargol impregnation (C–I). A, detail of the anterior body region, showing densely arranged basal bodies of somatic kineties and the unciliated V-shaped sucker lined by regularly spaced, oblique rows of highly refractive granules. B, detail of the posterior body region, showing the oral ciliature and the vacuolized cytoplasm. C, D, less-side overviews, showing the variability of body shape and size, as well as of the nuclear apparatus. E, F, I, details of the infundibular and peristomial ciliature, as well as of the nuclear apparatus, which is composed of an ellipsoidal macronucleus and two globular micronuclei. Arrowhead in (E, F) marks the curved anterior end of membranelles M1 and M2. G, somatic kineties are composed of narrowly spaced monokinetids. Asterisks mark irregularities in the somatic ciliary paưern. H, surface view, showing cortical granules. CP, cytopharynx; F, fibre; G, granules; M1–2, membranelle 1 and 2; MA, macronucleus; MI, micronuclei; OA, oral apparatus; OC, oral cilia; PM, paroral membrane; S, sucker; SK, somatic kineties. Scale bars = 5 µm (I), 10 µm (F, G), 15 µm (A, B), 40 µm (E), 50 µm (C, D).
Figure 1 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 1. Protoptychostomum simplex in vivo (A) and asser protargol impregnation (B–I). A, less-side view of a representative specimen. B, F–I, less-side overviews, showing the variability of body shape and size as well as of the nuclear apparatus (shaded grey) and sucker (shaded yellow). Dashed circles in (I) represent contractile vacuoles. C, oral ciliary paưern. The paroral membrane and both membranelles extend along the whole posterior body end to plunge into the infundibulum where they form a helix-like paưern. Membranelle M1 is made up of two rows of basal bodies and is not segmented. Membranelle M2 runs beside M1, is composed of only a single row of basal bodies and is not segmented. Arrowhead in (C) marks the curved anterior end of membranelles M1 and M2. D, E, ciliary paưern of the less (D) and the right (E) side. CP, cytopharynx; CV, contractile vacuoles; M1–2, membranelle 1 and 2; MA, macronucleus; MI, micronuclei; PM, paroral membrane; S, sucker; SK, somatic kineties. Scale bars = 30 µm (I), 40 µm (A, B, D, E), 80 µm (H), 100 µm (F, G).
Figure 3 in The search finds an end: the morphologically chimeric hysterocinetids belong to the subclass Hymenostomatia (Ciliophora: Oligohymenophorea)
Figure 3. Hysterocineta bellerophon in vivo (A) and asser protargol impregnation (B–L). A, less-side view of a representative specimen. B, oral ciliary paưern. Membranelle M1 is made up of two rows of basal bodies and runs only on the peristome. Membranelle M2 is cut in two segments: (i) the distal segment M2 is built from two rows of basal bodies and runs beside M1, (ii) the proximal segment M2' is composed of three rows of basal bodies and extends beside M3. Membranelle M3 consists of two rows of basal bodies and starts at the infundibular entrance. C–F, I–L, less-side overviews, showing the variability of body shape and size as well as of the nuclear apparatus (shaded grey) and sucker (shaded yellow). Dashed circles represent contractile vacuole. G, H, the ciliary paưern of the less (G) and the right (H) side. Arrows mark a posterior secant system each on the ventral and the dorsal margin of the right body side. Abbreviations: CV, contractile vacuole; IF, infundibulum; M1–3, membranelles 1–3; MA, macronucleus; PM, paroral membrane; S, sucker; SK, somatic kineties. Scale bars = 50 µm (A, G, H), 100 µm (C, D, E, F, I, J, K, L).
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Annotated Behaviour and Observability Dataset (ABODe)
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