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152 results for “mitochondrial DNA sequences”
Fig. 2 in Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography
Fig. 2. Strict consensus of 96 equally most-parsimonious trees (L 5 2198; CI 5 0.36; RI 5 0.80). Bootstrap support values are indicated above branches subtending species and conspecific haplogroups discussed in the text. For each terminal, country of origin, next-largest political unit (state, department, province, etc.), and an alphanumeric specimen identifier (from table 2) are provided. Numbers in parentheses refer to localities mapped in figure 1 and listed in the Gazetteer (appendix).
Figure 2. Phylogenetic relationships among the 29 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 2. Phylogenetic relationships among the 29 specimens of Orthometopon species. Individuals from two other terrestrial isopod species were used as outgroup taxa: Ligidium sp. and Armadillidium vulgare. Phylogenetic analyses, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), all produced trees with the same topology. Only the BI tree is presented here. Numbers above the branches indicate bootstrap values in the MP and ML analyses, respectively (MP/ML). Numbers below the branches indicate the posterior probabilities of the Bayesian analysis (BI).
Figure 1 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 1. Map showing the sampling localities of the 29 specimens used for the DNA analysis. The numbers correspond to those listed in Table 1.
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
<p>Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species-level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ('mitoenrichment'). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA ('targeted mitosequencing'). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38 to 2123-fold mean coverage. This produced complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible and can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.</p>
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
Open the record for dataset details and reuse information.
Mitochondrial DNA sequence phylogeny of Daucus
We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 17 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 17. Black adult male Bungarus candidus (UK B15) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Like the type specimen of Bungarus javanicus, it has a yellow ventral colouration and yellow spots on the vertebrals. Note unpigmented internasals and 5th and 6th supralabials of the right head side. Photo by Ulrich Kuch.
FIGURE 16 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 16. Close-up of a black adult male Bungarus candidus (UK BP4) from the area of Purwokerto, Central Java, Indonesia. Photo by Ulrich Kuch.
FIGURE 15 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 15. The most frequently encountered colour morph of "black" Bungarus candidus on Java represented by an adult male (UK BX3) from near Losarang (Kabupaten Indramayu, West Java, Indonesia). Photo by Ulrich Kuch.
FIGURE 13 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 13. Adult female Bungarus candidus (UK B34) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the anterior body and mosaic-like dark stippling on the posterior body and tail. Photo by Ulrich Kuch.
FIGURE 11 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 11. Adult male Bungarus candidus (UK B38) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced black bands on the posterior half of the body. Photo by Ulrich Kuch.
FIGURE 14 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 14. Adult male Bungarus candidus (UK B35) from the area of Losarang (Kabupaten Indramayu, West Java, Indonesia) with reduced bands on the posterior body and heavy pigmentation of all light interspaces and ventrolateral areas (opaque colouration is due to imminent shedding). Photo by Ulrich Kuch.
FIGURE 10 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 10. Regularly black-and-white banded juvenile Bungarus candidus from Desa Songgon, about 20 km SW of Banyuwangi, East Java, Indonesia. Note the characteristic light head pattern of juvenile specimens. Photo by Andrea Glässer-Trobisch and Dietmar Trobisch.
FIGURE 9 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 9. Black juvenile Bungarus candidus (ZMB 57702) from Banjar Berawa, Desa Canggu, Denpasar, Bali, Indonesia. Photo by Frank Tillack.
FIGURE 8 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 8. Ventral view of the partially leucistic juvenile Bungarus candidus (UK 96-1) from Linggarjati. Photo by Ulrich Kuch.
FIGURE 7 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 7. Juvenile Bungarus candidus (UK 96-1) from Linggarjati (Kabupaten Cirebon, West Java, Indonesia; 400– 500 m above sea level) with white snout, reduced black bands on anterior body, and white dorsals with dark tips on the rest of the body. Photo by Ulrich Kuch.
FIGURE 6 in The identity of the Javan Krait, Bungarus javanicus Kopstein, 1932 (Squamata: Elapidae): evidence from mitochondrial and nuclear DNA sequence analyses and morphology
FIGURE 6. Contour map of Java and Madura (Bali, adjacent to the east, not shown). Capital letters indicate collecting areas: A, Losarang (near Indramayu); B, area of the type locality of Bungarus javanicus (near Mt. Ciremai, e.g., Linggarjati); C, Purwokerto basin; D, coastal plain near Cilacap. Dots and circles, respectively, mark collecting localities of additional examined specimens and literature records of black-and-white banded Bungarus candidus.
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International Brain Laboratory public data
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OpenNeuro
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