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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 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).
Supplementary material 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
Table S1
Figure 3 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 3 Phylogenetic trees derived from Maximum-Likelihood (ML) and Neighbor Joining (NJ) approaches based on whole mitochondrial genomes. The numbers on the nodes are the bootstrap values of ML/NJ. The number after the species name is the GenBank Accession Number.
Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae)
<p>The Caribbean reef shark <i>Carcharhinus perezi</i> is a medium to large-bodied coastal and reef-associated predator found throughout the subtropical and tropical waters of the Atlantic Ocean and Caribbean Sea, although its populations are increasingly threatened by overfishing. We describe the first mitochondrial genome sequence for this species, using Illumina MiSeq sequencing of an individual from The Bahamas. We report the mitogenome sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA genes, 22 tRNA genes, 13 protein-coding genes, two non-coding genes; the control region and the origin of light-strand replication. We discuss the implications of this new information on future monitoring efforts and conservation measures such as marine protected areas, and urge future mitochondrial studies of sharks to expand their reach into the Atlantic Ocean.</p>
Figure 4 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure 4 A schematic of the structural organization of the mitochondrial control region in Lepus yarkandensis. Control region flanking genes tRNA-Phe and tRNA-Pro presented in red. Conserved elements in the control region denoted by gray boxes: TAS, termination associated sequence; CD, central conserved domain; CSB, conserved sequence block. SR, short repeat; LR, long repeat.
Figure 5 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure 5 Neighbor-joining and Bayes trees based on the complete mtDNA sequences of 25 lagomorphs. Values separated by slash (/) represent bootstrap support values for the NJ and Bayes trees.
Supplementary material 1 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure S1a, S1b
Figure 1 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure 1 Complete mitochondrial genome map of Lepus yarkandensis. Genes encoded on the heavy and light strands are shown outside and inside the circle, respectively.
Data from: Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)
Helicoidea is a diverse group of globally distributed land snails. While much is known regardingthe relationships of helicoid taxa, comparatively little is known about the evolution of themitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomesfrom Praticolella mexicana Perez, 2011 representing the first such data from the helicoid familyPolygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We foundthe mitochondrial genome of P. mexicana to be 14,008 bp in size, possessing the typical 37metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons, andmitogenome size and nucleotide content is consistent with other helicoid species. Our analysis ofgene order suggested that Helicoidea has undergone five mitochondrial rearrangements in thepast. Four rearrangements were limited to tRNA genes, including one homoplasticrearrangement in Helicidae and (Bradybaenidae+Camaena+P. mexicana). The fifthrearrangement, unique to Aegista, involved a protein coding gene.
Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences
Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here. Results: Phylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing the strong phylogenetic performance of random subsets of data also shown in this study. Phylogenetic results for both the 19-taxon and 44-taxon datasets corroborate previous hypotheses about the placement of Photobacterium and Aliivibrio within Vibrionaceae and also highlight problems with how Photobacterium is delimited and indicate that it likely should be dissolved into Vibrio to produce a phylogenetic taxonomy. The 19-taxon and 44-taxon trees based on the large chromosome are congruent for the majority of taxa that are present in both datasets. Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies. Conclusions: The phylogenetic analyses presented here represent the most comprehensive genome-level phylogenetic analyses in terms of taxa and data. Based on the availability of genome data for many bacterial species on GenBank, many other bacterial groups would also be amenable to similar genome-scale phylogenetic analyses even when present in multiple contigs. The result that collinear subsets of data are incongruent with the concatenated dataset and with each other while random data subsets show very little incongruence echoes the result of previous work on Shewanellaceae. The 44-taxon phylogenetic analysis presented here thus represents the future of phylogenomic analyses in scope and complexity.
Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
FIGURE 1 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes
FIGURE 1. Comparison of AT skews of Grylloidea, Gryllotalpoidea and Tettigonioidea.
FIGURE 7 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 7. Comparison of AT-skews and GC-skews of Eneopterinae and Gryllinae.
FIGURE 5 in Complete mitochondrial genome and taxonomic revision of Cardiodactylus muiri Otte, 2007 (Gryllidae: Eneopterinae: Lebinthini)
FIGURE 5. Map of the mitochondrial genome of Cardiodactylus muiri Otte, 2007.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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