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FIGURE 2 in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 2. Phylogenetic relationships of 14 Lumbricidae species, based on the nucleotide sequences of the 13 PCGs. Drawida japonica was included as an outgroup. Numbers at the branches represent Bayesian probabilities and bootstrap support (%). The blue clades represent unpigmented, the red ones pigmented specimens. The two unpigmented Korean specimens are marked in malachite-green.
FIGURE 1 in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 1. Phylogenetic relationships of 33 Crassiclitellata species, including E. nordenskioldi cf. pallida No. 1 and No. 3, based on the 13 PCG nucleotide sequences. Drawida japonica was included as an outgroup. Numbers at the branches represent ML bootstrap support.
Phylogenetic Analysis Based on the Complete Mitochondrial Genomes of Eight Nymphalidae Species (Lepi-doptera: Papilionoidea)
<p>Table S1: Basic sequence characteristics of mitochondrial genomes of eight newly sequenced species in Nymphalidae;</p> <p>Table S2: Base composition, AT content, AT-skew, GC-skew and total length (bp) of 105 species in all three codon positions, codon position 1, codon position 2 and codon position 3 in this study. The species highlighted in red are the ones that were sequenced;</p> <p>Table S3:<strong> </strong>Taxonomic information and GenBank accession numbers for 105 mitogenomes in Nymphalidae selected for characteristics and phylogenetic analysis in this study.</p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
Figure 2 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 2. Relative codon usage analysis for protein coding genes (PCGs) in the mitochondrial genome of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493 [top] and SRR14209494 [bottom]).
Figure 1 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 1. Circular DNA mitochondrial genome map of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493). The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: J.A. Guerrero.
Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution
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Data from: Evolutionary history of chimpanzees inferred from complete mitochondrial genomes
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Data from: The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ
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Data from: Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes
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Data from: The complete mitochondrial genome sequence of the Little Egret (Egretta garzetta)
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Data from: The complete sequence of the mitochondrial genome of Butomus umbellatus - a member of an early branching lineage of monocotyledons
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Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013
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Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
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Data from: Colonizing the wild west: low diversity of complete mitochondrial genomes in western North Pacific killer whales suggests a founder effect
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Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
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Data from: The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): characterization and comparative analysis
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Targeted sequencing and iterative assembly of near-complete genomes
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Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus
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International Brain Laboratory public data
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OpenNeuro
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