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opencc-by-sa-4.0Nov 2020View details →

mRNA expression data of genes related to mitochondrial quality control in hepatopancreas of the two marine bivalves, Mytilus edulis and Crassostrea gigas, during short-term hypoxia/reoxygenation stress

Coastal environments commonly experience strong oxygen fluctuations. Resulting hypoxia/reoxygenation stress can negatively affect mitochondrial functions, since oxygen deficiency impairs ATP generation, whereas a surge of oxygen causes mitochondrial damage by oxidative stress mechanisms. Marine intertidal bivalves are adapted to fluctuating oxygen conditions, yet the underlying molecular mechanisms that sustain mitochondrial integrity and function during oxygen fluctuations are not yet well understood. We used targeted mRNA expression analysis to determine the potential involvement of the mitochondrial quality control mechanisms in responses to short-term hypoxia (24 h at <0.01% O2) and subsequent reoxygenation (1.5 h at 21% O2) in two hypoxia-tolerant marine bivalves, the Pacific oysters Crassostrea gigas and the blue mussels Mytilus edulis. To test these hypotheses, We focused on the transcript levels of the following marker genes: for mitochondrial fission and fusion - mfn2 (encoding mitofusin 2),  opa1 (mitochondrial dynamin-like 120kDa protein), dnm1l (dynamin-1-like protein), mff  (mitochondrial fission factor), fis1 (mitochondrial fission protein 1); for protein and DNA quality control - tsfm (encoding mitochondrial translation elongation factor Ts), lonp1 (mitochondrial Lon protease),  spg7 (paraplegin), oma1 (mitochondrial metalloendopeptidase OMA1), clpB (mitochondrial caseinolytic matrix peptidase chaperone subunit B), atp23 (mitochondrial inner membrane protease ATP23), twnk (mitochondrial twinkle mtDNA helicase); and for mitophagy -  mieap (encoding mitochondrial eating protein), hyou1 (hypoxia upregulated protein 1), prkn (parkin), pink1 (PTEN- induced kinase 1), and pgam5 (mitochondrial serine/threonine protein phosphatase PGAM5). The revealed species-specific differences in the expression of the mitochondrial quality control pathways shed light on the potentially important mechanisms of mitochondrial protection against H/R-induced damage that might contribute to hypoxia tolerance in marine bivalves.

opencc-by-4.0Dec 2016View details →

Fig. 7. Maximum-likelihood tree for the mitochondrial DNA gene Cytochrome Oxidase C subunit 1 in A new species of the catfish Neoplecostomus (Loricariidae: Neoplecostominae) from a coastal drainage in southeastern Brazil

Fig. 7. Maximum-likelihood tree for the mitochondrial DNA gene Cytochrome Oxidase C subunit 1 for specimens of Neoplecostomus microps from rio Paraíba do Sul, rio Guapi- Açu and rio Macaé, and of Neoplecostomus paraty, using TN93+G model (n=21). Neoplecostomus paranensis and Neoplecostomus ribeirensis were used as outgroups.

opencc-by-4.0Aug 2011View details →

Fig. 2 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Fig. 2. The neighbour-joining (A) and Bayesian (B) trees for Suncus inferred from 1140 base-pairs of cytochrome b gene sequence. Bootstrap and posterior probability values are given above branches.

opencc-by-4.0Aug 2011View details →

Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.

opencc-by-4.0Dec 2016View details →

Figure 1 in Mitochondrial gene rearrangement within genus Gasteruption (Hymenoptera: Evanioidea: Gasteruptiidae)

Figure 1. Gene rearrangement in the Gasteruption spp. mitochondrial genomes. The red line shows reversal of gene. The black line shows translocation of gene. Translocation of trnN occurred between Gasteruption sp. and G. parvicollarium.

Figure 5 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Figure 5. Sternorrhyncha phylogenetic tree inferred from mitochondrial genome matrix. The phylogenetic tree were reconstruct using Bayesian inference method. Numbers at the nodes indicate Bayesian posterior probabilities.

Figure 4 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Figure 4. Comparison of the mitochondrial gene arrangement among Nipponaclerda biwakoensis, ancestral insect, other representative species of Psyllidae, Aphididae and Aleyrodidae and four public Coccocidea species.

Figure 2 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Figure 2. The codon number and relative synonymous codon usage (RSCU) in the Nipponaclerda biwakoensis mitochondrial genome.

Figure 1 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Figure 1. Gene map of the Nipponaclerda biwakoensis mitochondrial genome. Arrows indicate the orientation of gene transcription. The inner circles show G+C content.

Figure 3 in Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Figure 3. Predicted secondary structures of the 17 detected tRNA genes of Nipponaclerda biwakoensis mitochondrial genome. Watson–Crick pairs is indicated by lines, wobble GU pairs is indicated by dots and other noncanonical pairs is indicated by circles.

Figure 5 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 5. Comparison of the nucleotide sequences of the two putative control regions in the mitogenome of P. eriobotryae. The structural elements were recognized: repeat unit, TATA motif, TA(A)n motif, stem and loop, Poly T-stretch sequence, A + T-rich sequence and G(A)nT motif.

Figure 6 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 6. Gene rearrangement, transposition, inversion and inverse transposition. A. Comparison with the ancestor gene sequence of arthropods, Drosophila yakuba and P. eriobotryae gene sequence. B. Comparison with P. eriobotryae and other five known mitogenomes of Phlaeothripidae species. Yellow blocks show PCGs, blue ones show tRNA, red ones show rRNA and Colourless ones show CRs. Red dashes boxes represent conserve gene blocks. Red dotted ovals represent that the reverse transposition happened in the gene blocks. '+' indicates H-strand, and '-' indicates L-strand. Black arrows indicate the direction of gene translation.

Figure 1 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 1. The circular representation of the complete mitogenome of P. eriobotryae. The direction of gene transcription is indicated by the arrows. PCGs are showed as blue purple arrows, rRNA genes as green arrows, tRNA genes as pink purple arrow and CRs as orange arrows. The inner black circles show GC content and GC-skew plotted as the deviation from the average value of the entire sequence. The image was taken from slide-mounted specimen with an Olympus BX53 and edited manually in Adobe Photoshop 2022 v23.0.2.101.

Figure 4 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 4. Putative cloverleaf secondary structures of the 22 tRNAs of P. eriobotryae. The dot "." indicated mismatched base pairs.

Figure 3 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 3. The ratios of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks), and the ratio of Ka/Ks for each PCGs in the mitogenome of P. eriobotryae.

Figure 7 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 7. Phylogenetic tree of thrips obtained from Maximum-likelihood and MrBayes based on 13 PCGs dataset. The numbers on branches are superimposed with bootstrap support values (BP) and the Bayesian posterior probability (PP).

Figure 2 in Characterizing the complete mitochondrial genome of Psephenothrips eriobotryae Dang & Qiao (Thysanoptera: Phlaeothripidae) with massive gene arrangement in Phlaeothripidae

Figure 2. Codons distribution and usage in the mitogenome of P. eriobotryae. A. Amino acid composition: codon families are provided on the x-axis; numbers of codons of each amino acid are provided on the y-axis. B. The relative synonymous codon usage (RSCU).

opencc-by-4.0May 2017View details →

Fig. 5 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).

Fig. 5. Bayesian estimates of divergence times in scleractinians. The basal axis is a geologic time scale in units of million years ago (mya). Different time intervals are labeled with abbreviations (Cam, Cambrian; Ord, Ordovician; Sil, Silurian; Dev, Devonian; Car, Carboniferous; Per, Permian; Tri, Triassic; Jur, Jurassic; Cre, Cretaceous; Pal, Paleogene; Neo, Neogene). The chart below the phylogenetic tree gives the extinction rate (solid line) and origination rate (dashed line) in different geological periods, which were modified from Kiessling (2004) with major extinction events labeled with abbreviations (Rhae, Rhaetian; Plie, Pliensbachian; Kimm, Kimmeridgian; Ceno, Cenomanian; Maa, Maastrichtian, KT-extinction). Species with different types of intron are labeled with symbols: ●, Intron-729 (I729); ▲, Intron-893 (I893); ■, Intron-876 (I876).

opencc-by-4.0May 2017View details →

Fig. 4 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).

Fig. 4. Comparison of phylogenetic trees between the cox1 exon (left side) and intron (right side) in complex corals and corallimorpharians (A) and in sponges and robust corals (B). Tree topologies presenting the phylogenetic relationships of exons and introns were consensus trees between the maximum-likelihood analysis and Bayesian algorism. Numbers on branches are Shimedaira- Hasegawa-like/posterior probabilities. Dashed lines are potential changes in phylogenetic positions between the exon and intron trees.