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185 results for “Multigene”
Fig. 2A–O in Phylogenetic Analyses on the Tintinnid Ciliates (Protozoa, Ciliophora) Based on Multigene Sequence Data
Fig. 2A–O. Secondary structure of the internal transcribed spacer 2 (ITS2) RNA transcript of: A – Strombidinopsis sp.; B – Amphorellopsis acuta; C – Eutintinnus pectinis; D – Stenosemella nivalis; E – Codonellopsis nipponica; F – Tintinnopsis lohmanni; G – T. cylindrica; H – T. tubulosoides; I – Tintinnopsis sp. 2; J – Tintinnopsis sp. 1; K – Favella taraikaensis; L – F. ehrenbergii; M – F. campanula; N – Metacylis angulata and O – Tintinnopsis sp. 3. The diagram illustrates that all these species have a similar ITS2 secondary structure model – one palm with two fingers. Tintinnopsis sp. 1 and Tintinnopsis sp. 3 have the same ITS2 secondary structure, so are shaded together. Positions labeled II that lack a bulge are marked with arrows. Note that a bulge is present in this position in other species.
Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB
The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In the present study we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds, and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation, and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.
Supplementary material 1 from: Mantelatto FL, Pileggi LG, Pantaleão JAF, Magalhães C, Villalobos JL, Alvarez F (2021) Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868. ZooKeys 1047: 155-198. https://doi.org/10.3897/zookeys.1047.66933
Table S1
Figure 1 from: Mantelatto FL, Pileggi LG, Pantaleão JAF, Magalhães C, Villalobos JL, Alvarez F (2021) Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868. ZooKeys 1047: 155-198. https://doi.org/10.3897/zookeys.1047.66933
Figure 1 Concatenated phylogenetic tree of selected species of Macrobrachium representing wide geographical distribution of the group, based on the method of maximum likelihood of the 16S rDNA, COI mtDNA, 18S nDNA and H3 nDNA genes. Numbers on nodes refer to significance values of 1000 bootstrap replicates; values ≤ 50% are not shown. ARG: Argentina; BR: Brazil; CH: Chile; CR: Costa Rica; JAP: Japan; MX: México; NIG: Nigeria; PN: Panamá; VZ: Venezuela. ALD: Abbreviated larval development. ELD: Extended larval development. Blue: species from Indo-Pacific. Red: species from Africa. Green: former Cryphiops species.
Figure 6 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 6 Dorsal view of premaxilla and maxilla. ACambevadavisi, UFRJ 10713 BScleronemaoperculatum, UFRJ 11856. CScleronema sp1., UFRJ 10645. Scale bar: 1 mm max, maxilla; pre, premaxilla.
Figure 5 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 5 Left suspensory in dorsal view. ATrichomycterusgiganteus, UFRJ 5732, paratype. BCambevadavisi, UFRJ 10713. CTrichomycterusalternatus, UFRJ 5673. DCambevazonata, UFRJ 11900. ETrichomycterusbrasiliensis, UFRJ 4834. FCambevabrachykechenos, UFRJ 10586. GScleronemaoperculatum, UFRJ 11856. Scale bar: 1 mm hy, hyomandibula; iop, interopercle; mtg, metapterygoid; op, opercle; pop, preopercle.
Figure 4 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 4 Left lower jaw in medial view. ATrichomycterusgiganteus, UFRJ 5732, paratype. BCambevadavisi, UFRJ 10713. CTrichomycterusalternatus, UFRJ 9900. DCambevazonata, UFRJ 11900. ETrichomycterusbrasiliensis, UFRJ 4834. FCambevabrachykechenos, UFRJ 10586. GScleronemaoperculatum, UFRJ 11856. Scale bar: 1 mm aar, anguloarticuloretroarticular; corp.p, coronoid process; de, dentary; max.de.ch., maxillo-dentary channel; b.f. bone flap.
Figure 3 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 3 Cambevadavisi, topotype, UFRJ 9759, 67.6 mm SL; Brazil: Paraná: Balsa Nova. Photograph by A. M. Katz.
Figure 2 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 2 Phylogenetic positioning of Cambeva among the Trichomycteridae, inferred by Maximum Likehood from the analysis of molecular data, total of 4380 bp comprising segments of nuclear genes for GLYT, MYH6, RAG2 and SH3PX3 and the mitochondrial genes COI and CYTB. Numbers on each node are bootstrap percentages of the Maximum Likelihood analysis; asterisks indicate maximum support value and hyphen values under 50.
Figure 1 from: Katz AM, Barbosa MA, de Oliveira Mattos JL, da Costa WJE (2018) Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae). Zoosystematics and Evolution 94(2): 557-566. https://doi.org/10.3897/zse.94.29872
Figure 1 Phylogenetic positioning of Cambeva among the Trichomycteridae, inferred by Bayesian Inference from the analysis of molecular data, total of 4380 bp comprising segments of nuclear genes for GLYT, MYH6, RAG2 and SH3PX3 and the mitochondrial genes COI and CYTB. Numbers on each node represent posterior probabilities.
Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB
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Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species
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Data from: Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions
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Data from: Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes
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Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
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Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade
GEO Series GSE83850. Mus musculus. 38 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Multigene biomarkers of pyrethroid exposure: preliminary experiments: 15k microarrays
GEO Series GSE113284. Pimephales promelas. 144 samples. Type: Expression profiling by array.
Multigene biomarkers of pyrethroid exposure: preliminary experiments
GEO Series GSE113286. Pimephales promelas. 256 samples. Type: Expression profiling by array.
Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade [ATAC-Seq]
GEO Series GSE83847. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Rapid activation of distinct member of multigene families in Plasmodium spp.
GEO Series GSE128123. Plasmodium falciparum. 12 samples. Type: Expression profiling by array.
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