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Aligned Cox1 and Cob sequences from Oikopleura dioica and other tunicates.
<p>Supporting data for the manuscript « <em>Widespread use of the “ascidian” mitochondrial genetic code in tunicates</em> » containing a) assemblies of the cytochrome oxidase subunit 1 (Cox1) and cytochrome b (Cob) mitochondrial genes from ESTs downloaded from the Oikobase database and b) protein alignment of these sequences and other tunicate sequences to study which genetic code is used in tunicate mitochondria.</p>
Figure 5. Bayesian Inference tree calculated with complete cox1 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species
Figure 5. Bayesian Inference tree calculated with complete cox1 (1428 bp), cox3 (753 bp), and cytb (1127 bp) sequences of haemosporidian parasites and Klossiella equi (MH203050) and Klossia razorbacki (MT084562) as the outgroup. Bayesian posterior probabilities and Maximum Likelihood bootstrap values are indicated at most nodes. The scale bar indicates the expected number of substitutions per site according to the model of sequence evolution applied.
Figure 3. The maximum likelihood tree inferred from COX1 in Morphological and molecular evidences of Ascaridia galli in migratory quail Coturnix coturnix japonica from Baluchistan Pakistan
Figure 3. The maximum likelihood tree inferred from COX1 sequence (533 bp) of A. galli haplotypes and other Ascaridia species. Evolutionary analysis were conducted in MEGA 7. Scale bar shows genetic variation.
Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.
Fig. 4 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 4. Phylogenetic trees based on partial sequences from reported cox1 genes of insects according to NJ.
Fig.1 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig.1. PCR result of 18S rRNA of Lymantria dispar. Separated bands (from left to right). 18S1, 18S2, 18S rRNA, DL2000 marker.
Fig. 4 in Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas
Fig. 4. Molecular Phylogenetic analysis by Maximum Likelihood method. The evolutionary history was inferred using the ML method based on the General Time Reversible model. The phylogenetic tree illustrates COX1 gene sequences of nematodes related to A. pennula. Bootstrap values above 50 are shown in the tree. The tree is drawn to scale, with branch lengths measured in the number of substitutions-per-site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA7.
Fig. 1. A in Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas
Fig. 1. A. Caecum of the wild quail B. Morphology of male and female caecal worm. All the parts of male and female caecal worm Aulonocephalus pennula are marked in Fig. 1B.
Fig. 3 in Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas
Fig. 3. Pairwise alignment of the sequences of A. pennula and H. gallinarum. Sequence variations between A. pennula and H. gallinarum are highlighted in red. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 2. A in Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas
Fig. 2. A. PCR amplification of COX1 gene using nematode primers. Lane M: 100 bp DNA ladder (Fermentas); lane 1‾4 COX1 gene amplicon (750 bp). B. PCR amplification of partial COX1 gene using gene specific primers. Lane M: 100 bp DNA Marker (Fermentas); lane 1‾4 partial COX1 amplified products (405bp).
Fig. 2 Maximum likelihood phylogenetic tree constructed using the mitochondrial cox1 gene for 103 in Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary
ƒFig. 2 Maximum likelihood phylogenetic tree constructed using the mitochondrial cox1 gene for 103 Dictyocaulus lungworms originating from Hungary and five lungworms from GenBank indicated by their accession numbers (one dictyocaulid worm of red deer in New Zealand and four sequences of D. viviparus). Lungworms were collected from hunted deer (fallow, red and roe deer), indicated by triangle, square and circle, respectively. Geographical collecting regions are indicated for each sample
Fig. 9. Phylogenetic relationships among primate pinworms inferred from cox1 in A pinworm's tale: The evolutionary history of Lemuricola (Protenterobius) nycticebi
Fig. 9. Phylogenetic relationships among primate pinworms inferred from cox1 gene sequences. Numbers at the nodes represent ML/NJ bootstrap values, respectively.
Fig. 2. Simplified neighbor-joining tree reconstructed from partial cox1 in Lurking in the dark: Cryptic Strongyloides in a Bornean slow loris
Fig. 2. Simplified neighbor-joining tree reconstructed from partial cox1 gene (716 bp) sequences of Strongyloides spp. S. fuelleborni sequences for Bornean primates cluster within the S. fuelleborni group, together with previously described sequences for the parasite found in African and Japanese primates. The S. stercoralis cluster includes sequences from humans from Laos, Africa and Japan, captive chimpanzees, and dogs. The Strongyloides sp. cluster corresponds to sequences from the slow loris. An alternative hypothesis is presented next to the tree, where instead of representing a different species, Strongyloides sp. would be part of a cryptic assemblage within the S. stercoralis group.
Fig. 3. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the cox1 in Detection of maize bushy stunt phytoplasma in leafoppers collected in native corn crops grown at high elevations in southeast Mexico
Fig. 3. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the cox1 mini-barcode sequences obtained for the red speckled nymphs and Idiodonus wickhami (Hemiptera: Cicadellidae) (both marked with a circle) with reference sequences from GenBank. Bar 5 substitution in 100 positions.
Fig. 1 in Sarcocystis cruzi infection in free-living European bison (Bison bonasus bonasus L.) from the Białowieza˙Forest, Poland - A molecular analysis based on the cox1 gene
Fig. 1. Overview of consistent nucleotide differences between two cox1 gene sequences of S. cruzi MW490605 and MW490606. Numbers above and below the sequences refer to nucleotide positions in the two GenBank sequences used in the comparison. Positions where the two sequences were identical are signified with Dots (.).
Fig. 2 in Sarcocystis cruzi infection in free-living European bison (Bison bonasus bonasus L.) from the Białowieza˙Forest, Poland - A molecular analysis based on the cox1 gene
Fig. 2. Phylogenetic tree for selected Sarcocystis cruzi isolates and selected members of Sarcocystis species found in Bovidae based on partial sequences of cox1 using the maximum parsimony method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. GenBank accession numbers are listed next to the taxon names. The country of origin of S. cruzi isolates are listed in brackets.
Fig. 2. Cox1 in Sarcocystis sp. shed by the common boa snake (Boa constrictor) in Brazil
Fig. 2. Cox1-based evolutionary analysis of Sarcocystis spp.: The tree was inferred by using the Maximum Likelihood method and Tamura 3-parameter model. A discrete Gamma distribution was used to model evolutionary rate differences among sites. The tree with the highest log likelihood is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. This analysis involved 31 nucleotide sequences. All positions containing gaps and missing data were eliminated (complete deletion option). Branches marked with (•) contain sequences detected in snakes. The numbers between parenthesis represent the number of identical sequences at each terminal node. The names between parenthesis represent the hosts in which each sequence at terminal node was found. There were 807 positions in the final dataset. Evolutionary analyses were conducted in MEGA X.
Fig. 2. Maximum likelihood tree constructed from partial cox1 in Spirometra infection in a captive Samar cobra (Naja samarensis) in the United States: An imported case?
Fig. 2. Maximum likelihood tree constructed from partial cox1 gene sequences of Spirometra samples and related taxa. HKY + G + I was used as the best substitution model. Schistocephalus solidus and Dibothriocephalus nihonkaiensis were used as outgroups. (JPN – Japan; KOR – South Korea; CHI and CHN – China; AUS – Australia; IRA – Iran; USA – United States; THA – Thailand; MMR – Myanmar; TZA – Tanzania; IND – India; VNM – Vietnam; KHM – Cambodia; LAO – Laos; COL – Colombia; NZL – New Zealand; IDN – Indonesia; ROU – Romania; SSD – South Sudan; ETH – Ethiopia; POL – Poland; UKR – Ukraine; FIN – Finland; CHL – Chile; BRA – Brazil).
Fig. 2. Haplotype network constructed using cox1 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 2. Haplotype network constructed using cox1 (744 bp) gene sequences of T. hydatigena. Seven haplotypes formed by the T. hydatigena isolates obtained in this study: (Hap 1-Hap 7). Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Figure 3 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 3. Phoronid phylogeny. Most probable Bayesian likelihood tree (P = 0.68) from analysis of the 13tx alignment with clade credibility values from the majority rule consensus tree, which had the same topology. Where two clade credibility values are shown the first was from a run with the chiton as outgroup (not shown), and the second from a run with Phoronis ovalis as outgroup. MrBayes run commands were: charset coding_1st = 1-621\3; charset coding_2nd = 2-621\3; charset coding_3rd = 3-621\3; charset non-coding = 622-4515; partition all_4 = 4: coding_1st, coding_2nd, coding_3rd, non-coding; set partition = all_4; lset applyto=(all) nst = 6 rates = invgamma; databreaks 621 2386; unlink shape = all, pinvar = all, statefreq = all, revmat = all; prset ratepr = variable; mcmc ngen = 106 samplefreq = 100 printfreq = 5000 savebrlens = yes; plot match = all; sumt burnin = 2002. The tree shown was drawn in PAUP*4. The.con file was imported and displayed as a phylogram. Clade credibility values were added in a graphics editor.
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