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FIG. 4 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 4. Phylogenetic trees of 17 piciform species based on the amino acid dataset. The numbers abutting branches refer to Bayesian posterior probabilities (left) and ML bootstraps (right), ‾ not recovered. Branch lengths and topology are from the BI analysis. Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.

FIG. 2 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 2. Genetic distance within subfamily, between subfamily and family. Each boxplot represents the P distance based on the nucleotide and the amino acid datasets from 13 mitochondrial PCGs. Lower horizontal bar represents smallest observation, lower edge of rectangle represents 25 percentile, central bar within rectangle represents median, upper edge of rectangle represents 75 percentile, upper horizontal bar represents largest observation.

FIG. 1 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 1. Circular map of the J. torquilla mitogenome. The inner circle shows the GC content, which is calculated based on a window-sliding method. The outer circle shows the gene features, orange for rRNA, red for tRNA, and blue for CDS. Genes inside the circle (on the J strand) are transcribed clockwise, while the outsides (on the N strand) are transcribed counterclockwise.

FIG. 3 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 3. Phylogenetic trees of 17 piciform species based on the nucleotide dataset inferred from Bayesian inference (a) and maximum likelihood (b). The numbers abutting branches refer to Bayesian posterior probabilities (BPP) and bootstrap support (BS). Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.

opencc-zeroNov 2020View details →

Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus

The Atlantic blue crab, Callinectes sapidus, is an estuarine keystone species that functions as both predator and prey in food webs and supports a multi-million dollar fishery along the western Atlantic coast from the US mid-Atlantic to southern Brazil. Throughout their range, blue crabs are host to viral, bacterial, fungal, protozoan, and metazoan pathogens. Reoviruses are non-enveloped icosahedral viruses with genomes comprised of 9 to 12 segments of linear double-stranded RNA (dsRNA). They have been found in diverse host species including brachyuran crustaceans. This work describes the sequence of a novel reovirus genome, discovered in Callinectes sapidus. The double-stranded RNA genome of CsRV2 consists of 12 segments that encode 13 putative proteins. High nucleotide sequence identity with Eriocheir sinensis Reovirus 905 revealed this virus belongs to Cardoreovirus within the Reoviridae family.

opencc-zeroDec 2016View details →

Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.

opencc-zeroDec 2012View details →

Data from: Complete mitochondrial genome of the poorly known Amur sculpin Mesocottus haitej (Cottoidei: Cottidae)

The complete mitochondrial genome sequence of Mesocottus haitej has been obtained by the next generation sequencing, which contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and non-coding control region with the total length of 16,527 bp. The gene content, arrangement, codon usage and base composition of M. haitej mitogenome have no unusual features that distinguish it from most other teleost fishes. According to the result of a pilot phylogenetic analysis, the freshwater Mesocottus is a sister lineage to the Cottus clade. The new mitogenomic data could provide useful information for the further studies on molecular systematics and conservation genetics of cottids.

opencc-zeroDec 2012View details →

Data from: The complete sequence of the mitochondrial genome of Butomus umbellatus - a member of an early branching lineage of monocotyledons

In order to study the evolution of mitochondrial genomes in the early branching lineages of the monocotyledons, i.e., the Acorales and Alismatales, we are sequencing complete genomes from a suite of key taxa. As a starting point the present paper describes the mitochondrial genome of Butomus umbellatus (Butomaceae) based on next-generation sequencing data. The genome was assembled into a circular molecule, 450,826 bp in length. Coding sequences cover only 8.2% of the genome and include 28 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA genes and a 16S rRNA gene are transferred from the plastid genome. However, the total amount of recognized plastid sequences in the mitochondrial genome is only 1.5% and the amount of DNA transferred from the nucleus is also low. RNA editing is abundant and a total of 557 edited sites are predicted in the protein coding genes. Compared to the 40 angiosperm mitochondrial genomes sequenced to date, the GC content of the Butomus genome is uniquely high (49.1%). The overall similarity between the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest relative yet sequenced, is low (less than 20%), and the two genomes differ in size by a factor 2. Gene order is also largely unconserved. However, based on its phylogenetic position within the core alismatids Butomus will serve as a good reference point for subsequent studies in the early branching lineages of the monocotyledons.

opencc-zeroDec 2013View details →

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

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 are presented along with annotation and characterization of intragenomic single nucleotide polymorphism (SNPs) and indel variation.

opencc-zeroDec 2009View details →

Data from: Evolutionary history of chimpanzees inferred from complete mitochondrial genomes

Investigations into the evolutionary history of the common chimpanzee, Pan troglodytes, have produced inconsistent results, due to differences in the types of molecular data considered, the model assumptions employed, and the quantity and geographical range of samples used. We amplified and sequenced 24 complete P. troglodytes mitochondrial genomes from fecal samples collected at multiple study sites throughout sub-Saharan Africa. Using a 'relaxed molecular clock,' fossil calibrations, and 12 additional complete primate mitochondrial genomes, we analyzed the pattern and timing of primate diversification in a Bayesian framework. Our results support the recognition of four chimpanzee subspecies. Within P. troglodytes, we report a mean (95% highest posterior density (HPD)) time since most recent common ancestor (tMRCA) of 1.026 (0.811-1.263) MYA for the four proposed subspecies, with two major lineages. One of these lineages (tMRCA = 0.510 [0.387-0.650] MYA) contains P. t. verus (tMRCA = 0.155 [0.101-0.213] MYA) and P. t. ellioti (formerly P. t. vellerosus; tMRCA = 0.157 [0.102-0.215] MYA), both of which are monophyletic. The other major lineage contains P. t. schweinfurthii (tMRCA = 0.111 [0.077-0.146] MYA), a monophyletic clade nested within the P. t. troglodytes lineage (tMRCA = 0.380 [0.296-0.476] ¬MYA). We utilized two analysis techniques that may be of widespread interest. First, we implemented a Yule speciation prior across the entire primate tree with separate coalescent priors on each of the chimpanzee subspecies. The validity of this approach was confirmed by estimates based on more traditional techniques. We also suggest that accurate tMRCA estimates from large, computationally difficult sequence alignments may be obtained by implementing our novel method of bootstrapping smaller, randomly sub-sampled alignments.

opencc-zeroDec 2013View details →

Data from: Evolutionary relationships within the Triops (Notostraca: Branchiopoda) using complete mitochondrial genomes

The tadpole shrimp (Notostraca: Triops) have been called living fossils with conserved morphology, but subtle morphological variations within and between species has yielded confused taxonomic assignments. To aid in cryptic species detection of tadpole shrimp from southern New Mexico, USA, the first complete mitochondrial genomes for three putative species (T. longicaudatus "long," T. l. "short," T. newberryi) are reported. The genomes ranged in length from 15,058 bp to 15,060 bp with 13 coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Phylogenetic trees were constructed using previously sequenced Triops-genomes to assess genetic relationships within the genus. The T. longicaudatus-genomes from Genbank were consistent with our genomes for T. newberryi and T. l. "short." Variation in mitochondrial genes were identified that will aid future identification of cryptic lineages of tadpole shrimp. Genetic differentiation among the genomes of Triops in New Mexico support elevation to species status.

FIGURE 5 in Complete mitochondrial genome of a Neotropical dobsonfly Chloronia mirifica Navás, 1925 (Megaloptera: Corydalidae), with phylogenetic implications for the genus Chloronia Banks, 1908

FIGURE 5. Phylogenetic relationships among the dobsonfly genera inferred from mt genome sequences. Numbers at the nodes are Bayesian posterior probabilities (left) and ML bootstrap values (right).

FIGURE 3 in Complete mitochondrial genome of a Neotropical dobsonfly Chloronia mirifica Navás, 1925 (Megaloptera: Corydalidae), with phylogenetic implications for the genus Chloronia Banks, 1908

FIGURE 3. Predicted secondary structure of the rnnL in the Chloronia mirifica mt genome. Roman numerals denote the conserved domain structure. Dash (-) indicates Watson-Crick base pairing and dot () indicates G-U base pairing.

FIGURE 1 in Complete mitochondrial genome of a Neotropical dobsonfly Chloronia mirifica Navás, 1925 (Megaloptera: Corydalidae), with phylogenetic implications for the genus Chloronia Banks, 1908

FIGURE 1. Mitochondrial map of Chloronia mirifica. Circular maps were drawn with CGView (Grant et al. 2008). The arrows indicated the orientation of gene transcription. The tRNAs are denoted by the color blocks and are labelled according to the IUPACIUB single-letter amino acid codes (L1: UUR; L2: CNU; S1: AGN; S2: UCN). The GC content was plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. GC-skew was plotted as the deviation from the average GC-skew of the entire sequence. The inner cycle indicated the location of the genes in the mt genome.

FIGURE 2 in Complete mitochondrial genome of a Neotropical dobsonfly Chloronia mirifica Navás, 1925 (Megaloptera: Corydalidae), with phylogenetic implications for the genus Chloronia Banks, 1908

FIGURE 2. Inferred secondary structure of 22 tRNAs in the Chloronia mirifica mt genome. Most tRNAs are labeled with the abbreviations of their corresponding amino acids. Dash (-) indicates Watson-Crick bonds and dot () indicates GU bonds.

FIGURE 4 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes

FIGURE 4. Phylogenetic reconstruction of the Ensifera using mitochondrial PCGs and rRNAs concatenated dataset. (A) Maximum likelihood result; (B) Bayesian result.

FIGURE 3 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes

FIGURE 3. Mitogenome organization across sequenced Ensifera. Genome organization of (A) most sequenced ensiferans and proposed insect ancestor; (B) Gryllinae species; (C) the two Sinochlora species; (D) Phyllomimus detersus of Pseudophyllinae; (E) Ruidocollaris obscura of Phaneropterinae. The circular mitogenomes are linearized to do better presentation. The translocated regions are highlighted in color. Gene lengths are not to scale.

FIGURE 2 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes

FIGURE 2. Potential stem-loop structures and their location of Gryllidea. (A) the location of the predicted stem-loop in the mitogenome of Gryllidea, (B) potential stem-loop structures of cricket mitogenomes from Gryllidea

opennotspecifiedDec 2017View details →

FIGURE 4 in The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea

FIGURE 4. Predicted secondary structure of the lrRNA gene in Styloperla spinicercia. Roman numerals represent the conserved domain structures. Dashes (–) indicate Watson–Crick base pairings and () indicates G-U base pairing.