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865 results for “Mitochondrial genomes”
Figure 5 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 5 Bayesian tree constructed based on 86 whole-mitochondrial sequences of Lateolabrax maculatus. Each line represents one individual in the population. The reseda area and orange area represent north population and south population, respectively. Lateolabrax japonicus was used as outgroup.
Figure 6 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 6 The median-joining network constructed based on 78 haplotypes of Lateolabrax maculatus. Each cycle represents a haplotype, the area of the circle is proportional to the frequency of haplotype. Different geographical populations were shown in different colors.
Figure 3 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 3 Plot of pairwise estimates of genetic (FST) and geographical distance between populations of Lateolabrax maculatus.
Figure 4 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 4 Admixture analysis among all populations derived from 85 whole-mitochondrial sequences. The K value was set 2 and 3.
Figure 2 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 2 The structure of Lateolabrax maculatus mitochondrial genome. The total length of mitochondrial genome of L. maculatus was 16,601 bp comprising 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes. 249 high-confidence single nucleotide polymorphism (SNP) sites and 24 indels was identified in 85 individuals.
Figure 1 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 1 Locations of 12 sampling sites of Lateolabrax maculatus. 85 individuals of L. maculatus were collected from 12 geographic locations including Tianjin (TJ), Yantai (YT), Wendeng (WD), Lianyungang (LY), Zhoushan (ZS), Wenzhou (WZ), Shantou (ST), Shenzhen (SZ), Zhanjiang (ZJ), Haikang (HK), Tieshan (TS), Fangcheng (FC) along Chinese coastal waters. The average sea surface temperature (SST) of 1981-2010 at 12 sampling sites were retrieved from NOAA Optimum Interpolation (OI) Sea Surface Temperature (SST) V2 (https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.html).
Supplementary material 1 from: Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G (2020) Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). ZooKeys 969: 23-42. https://doi.org/10.3897/zookeys.969.49278
Tables S1–S7
Figure 3 from: Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G (2020) Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). ZooKeys 969: 23-42. https://doi.org/10.3897/zookeys.969.49278
Figure 3 The long polythymine stretch and conserved sequence blocks in the A+T rich regions from four species. Note: The long polythymine stretch. T-stretch sequence was labelled with box, located in the majority strand. Within each block, nucleotides identical in the two sequences are bottom-marked with asterisks.
Supplementary material 2 from: Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G (2020) Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). ZooKeys 969: 23-42. https://doi.org/10.3897/zookeys.969.49278
Figures S1–S4
Supplementary material 1 from: Macher J-N, Drakou K, Papatheodoulou A, Hoorn B, Vasquez M (2020) The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. Metabarcoding and Metagenomics 4: e58259. https://doi.org/10.3897/mbmg.4.58259
Scripts used for Megahit and Spades assemly of mitochornial genomes and nuclear 18S and 28S rRNAs
Alignment used for the phylogenies of "The earliest diverging extant scleractinian corals recovered by mitochondrial genomes"
<p>Alignment of scleractinian corals based on mitochondrial genomes and including species of the family Micrabaciidae. This alignment was used for running Maximum Likelihood and Bayesian Inference phylogenies. "tree02_alignment.phy" refers to the actual alignment while "tree02_alignment.partitions.txt" indicates where each gene partition begins/ends.</p>
The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)
<p>Pyralidae is the largest family in Lepidoptera, with more than 25,000 species in the world, some of which are pests of agricultural and forestry plants, such as <em>Orthaga</em> (Yang et al. 2020)<em>. Orthaga achatina</em> Butler (Lepidoptera: Pyralidae) is the most serious pest of camphor trees (<em>Cinnamomum camphora</em>) in China, Korea, Japan, and Malaysia (Wu 2006). <em>O. achatina</em> can also feed on other Lauraceae plants, such as <em>Lindera glauca</em> and <em>Cinnamomum cassia</em>, causing serious defoliates (Long et al. 2017). The mitochondrial genomes have the potential to be “molecular clock” due to its high mutation rate and low DNA recombination rate (Gai et al. 2020; Yang et al. 2020). However, the mitochondrial genome of <em>O. achatina</em> has not been publicly reported. Therefore, we determined to sequence the complete mitochondrial genome of <em>O. achatina</em> using the <em>de novo</em> sequencing techniques strategy to understand the mitogenomic background and genetic evolution relationship of<em> O. achatina</em>.</p> <p> </p> <p>In the present study, samples of <em>O. achatina</em> were collected from camphor trees in July 2020 in Suzhou, Jiangsu Province, China (N31.16568<sup>o</sup>, E120.62638<sup>o</sup>). Some of these samples were immediately frozen at -80°C for sequencing analysis and others were preserved in the Entomological Lab of Nanjing Forestry University, and their specimen code is 2020NJEM1855-1860. The genomic DNA was extracted from <em>O. achatina</em> using CTAB (cetyltrimethylammonium Ammonium Bromide) method (Huanca-Mamani et al. 2015). Raw data generated by the Illumina HiSeq platform (Illumina Inc.; San Diego, CA, USA) were subject to <em>de novo</em> assembly by SPAdes version 3.14 (Bankevich et al. 2012). The complete mitochondrial genomes were annotated by MITOS WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) (Bernt et al. 2013) and submitted to NCBI GenBank (GenBank accession number: MT916176).</p> <p> </p> <p>The mitochondrial genome of <em>O. achatina</em> was 15,150 bp in size, with a nucleotide composition of 38. 9% A, 41.8% T, 11.4% C and 7.9% G. The mitochondrial genome of <em>O. achatina</em> comprised the entire set of 37 typical invertebrate mitochondrial genes consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (D-loop). The majority-coding strand encoded 23 genes (9 PCGs and 14 tRNAs), whereas the minority-coding strand encoded 14 genes (4 PCGs, 8 tRNAs, and 2 rRNAs). The sequence and arrangement of genes were highly conserved, suggesting the similarity with typical characteristics of the genome in Lepidoptera (Liu et al. 2018; Wu et al. 2016, 2020). A total of 44 overlapping nucleotides between genes in 6 locations with a length of 2 to 25 bp were found, whereas there were 857 bp intergenic nucleotides in 22 locations, ranging from 4 to 297 bp in length.</p> <p> </p> <p>All protein-coding genes (PCGs) were initiated with ATN as the start codon except the <em>cox1</em>, which is no justification for continued speculation about polynucleotide start codon similar to other Lepidoptera insects (Liu et al. 2018; Singh et al. 2017; Yang et al. 2020). Ten PCGs had canonical stop codons TAA or TAG, while three had incomplete termination codons single T (<em>cox3</em> and <em>atp6</em>) or TA (<em>nad4L</em>). There were 22 tRNA genes with a length between 63 and 70 bp. All tRNA genes exhibited a typical clover-leaf secondary structure, except for tRNA-Ser(AGN) lacking the dihydrouridine (DHU) arm, which is common in Lepidoptera insects (Garey and Wolstenholme 1989). The lengths of lrRNA and srRNA were 1,362 bp and 780 bp, respectively. The control region was located between srRNA and tRNA-Met with a total length of 298 bp.</p> <p> </p> <p>In addition, the BLAST-based ortholog detector OrthoFinder v2.2.7 (Emms and Steven 2019) with default parameter values were used to identify ortholog among all the protein sequences of the 24 mitochondrial genomes. The phylogenetic relationship of <em>O. achatina</em> and 23 Lepidoptera species was inferred from phylogenetic analysis of the 13 protein-coding genes using MEGA7.0 software with maximum likelihood method and 1000 replicate sets on bootstrap analysis. The amino acid identity (AAI) of the 13 protein-coding genes of each Lepidoptera species and <em>O. achatina</em> were calculated by NCBI BLASTP. The phylogenetic tree and AAI heatmap of each protein was visualized using EVOLVIEW version 2 (<a href="https://evolgenius.info/evolview-v2/#login">https://evolgenius.info//evolview-v2</a>) (He et al. 2016). Phylogenetic analyses showed similar relationships among sampled families as shown in Yang et al. (2020). Each clade showed a monophyletic cluster and the following clades were highly supported (Fig 1): (1) Pyralidae + Crambidae; and (2) (Pyralidae + Crambidae) + (Noctuidae + (Bombycidae + Geometridae)). We also found that <em>O. achatina</em> strains had the closest relationship with the genus <em>Hypsopygia</em> and <em>Endotricha</em>, which were located in a clade in the clade of Pyralidae. This study can provide a useful resource for the genetic evolution of <em>O. achatina </em>and underline the potential importance of mitochondrial genomes in comparative genomic analyses of Lepidoptera species.</p>
Supplementary material 1 from: Qi L, Kong L, Li Q (2020) Redescription of Stenothyra glabra A. Adam, 1861 (Truncatelloidea, Stenothyridae), with the first complete mitochondrial genome in the family Stenothyridae. ZooKeys 991: 69-83. https://doi.org/10.3897/zookeys.991.51408
Relative synonymous codon usage (RSCU) of each amino acid in the mitogenome of S. glabra
Supplementary material 2 from: Qi L, Kong L, Li Q (2020) Redescription of Stenothyra glabra A. Adam, 1861 (Truncatelloidea, Stenothyridae), with the first complete mitochondrial genome in the family Stenothyridae. ZooKeys 991: 69-83. https://doi.org/10.3897/zookeys.991.51408
Secondary structure of tRNA in S. glabra mitogenome
Figure 1 from: Qi L, Kong L, Li Q (2020) Redescription of Stenothyra glabra A. Adam, 1861 (Truncatelloidea, Stenothyridae), with the first complete mitochondrial genome in the family Stenothyridae. ZooKeys 991: 69-83. https://doi.org/10.3897/zookeys.991.51408
Figure 1 Stenothyra glabra A. Adams, 1861 A shell LSGB-G1801-4 B exterior surface of operculum C protoconch D, E radula. Scale bars: 1 mm (A); 200 μm (B), 200 μm (C), 20 μm (D), 10 μm (E).
Figure 3 from: Qi L, Kong L, Li Q (2020) Redescription of Stenothyra glabra A. Adam, 1861 (Truncatelloidea, Stenothyridae), with the first complete mitochondrial genome in the family Stenothyridae. ZooKeys 991: 69-83. https://doi.org/10.3897/zookeys.991.51408
Figure 3 Summary tree from Maximum Likelihood analysis of concatenated COI, 16S and 28S sequences. Support indices are BI posterior probabilities (above nodes, > 0.9) and ML bootstraps (below nodes, > 70).
Figure 5 from: Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H (2020) Sequence and organisation of the mitochondrial genome of Japanese Grosbeak (Eophona personata), and the phylogenetic relationships of Fringillidae. ZooKeys 995: 67-80. https://doi.org/10.3897/zookeys.995.34432
Figure 5 The phylogenetic tree generated for 17 species of Fringillidae. The values indicated at the nodes are Bayesian posterior probabilities (left) and ML bootstrap proportions (right).
Figure 1 from: Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H (2020) Sequence and organisation of the mitochondrial genome of Japanese Grosbeak (Eophona personata), and the phylogenetic relationships of Fringillidae. ZooKeys 995: 67-80. https://doi.org/10.3897/zookeys.995.34432
Figure 1 Circular map of the mitochondrial genome of Eophona personata. tRNAs are denoted as one-letter symbols according to IUPAC-IUB single-letter amino acid codes; L1 = UUR, L2 = CUN, S1 = UCN, S2 = AGY.
Figure 2 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 2 Comparison of codon usage in mitochondrial genomes of Onychostoma lepturuma Relative synonymous codon usage (RSCU) in the Onychostoma lepturum mitogenome. Codon families are provided on the X-axis, and the RSCU values, on the Y-axis b Codon distribution in the Onychostoma lepturum mitogenome. CDspT, codons per thousand codons. Codon families are provided on the X-axis.
Figure 1 from: Wang I-C, Lin H-D, Liang C-M, Huang C-C, Wang R-D, Yang J-Q, Wang W-K (2020) Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. ZooKeys 1005: 57-72. https://doi.org/10.3897/zookeys.1005.57592
Figure 1 Gene map of the mitochondrial genome of Onychostoma lepturum. Two rRNA genes (in red); 13 coding genes (in green); 22 tRNA genes and control region (D-loop) (in yellow). (Color figure online).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.