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Ecol Evol
2018 Nov 01;822:10673-10686. doi: 10.1002/ece3.4427.
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The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida.
Mu W
,
Liu J
,
Zhang H
.
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Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world''s oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep-sea member of the order Brisingida. Similar to other starfish, it contained 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty-two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep-sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila''s adaptation to deep-sea environment.
Figure 1. Mitochondrial gene map of Freyastera benthophila. All of 37 genes are encoded on the both strands. Genes for proteins and rRNAs are shown with standard abbreviation. Genes for tRNAs are designated by a single letter for the corresponding amino acid with two leucine tRNAs and two serine tRNAs differentiated by numerals
Figure 2. The synteny and identity level of Freyastera benthophila mitogenome against each of the other seven starfish mitogenomes. Ideograms and ribbons represent the similarity pairwise blastn searches. In F. benthophila ideogram, the 13 coding genes are colored in blue, control regions are colored in black, and rRNAs are colored in green. The figure was produced using Circoletto (Darzentas, 2010). FB (F. benthophila), AB (Acanthaster brevispinus), AP1 (Acanthaster planci), AJ (Aphelasterias japonica), AA (Asterias amurensis), AP2 (Astropecten polyacanthus), LQ (Luidia quinaria), PP (Patiria pectinifera)
Figure 3. Codon usage in Freyastera benthophila. All codons for amino acids have been classified. Each amino acid is designated by a single letter for the corresponding codon. xâ€axis and yâ€axis represent the used times of each codon
Figure 4. Comparison of mitochondrial gene arrangement in Echinodermata. The bars show identical gene blocks. The noncoding regions are not presented, and gene segments are not drawn to scale
Figure 5. Phylogenetic trees based on the concatenated amino acids of 13 proteinâ€coding genes. The branch length is determined with NJ analysis. Antedon mediterranea was used as outâ€group. NJ (left number) and ML (right number) bootstrap values are given for each branch. The red dot highlights the species sequenced in this study
Adkins,
Evolution of the primate cytochrome c oxidase subunit II gene.
1994, Pubmed
Adkins,
Evolution of the primate cytochrome c oxidase subunit II gene.
1994,
Pubmed
Arndt,
Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria.
1998,
Pubmed
,
Echinobase
Asakawa,
Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome.
1995,
Pubmed
,
Echinobase
Bernt,
MITOS: improved de novo metazoan mitochondrial genome annotation.
2013,
Pubmed
Boore,
Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa.
2000,
Pubmed
Boore,
Sequencing and comparing whole mitochondrial genomes of animals.
2005,
Pubmed
Boore,
Animal mitochondrial genomes.
1999,
Pubmed
Boore,
Big trees from little genomes: mitochondrial gene order as a phylogenetic tool.
1998,
Pubmed
Brandt,
Energy converting NADH:quinone oxidoreductase (complex I).
2006,
Pubmed
Bridge,
Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.
1992,
Pubmed
Cantatore,
The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.
1989,
Pubmed
,
Echinobase
Conant,
GenomeVx: simple web-based creation of editable circular chromosome maps.
2008,
Pubmed
da Fonseca,
The adaptive evolution of the mammalian mitochondrial genome.
2008,
Pubmed
Dahlgren,
Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria.
2016,
Pubmed
Darzentas,
Circoletto: visualizing sequence similarity with Circos.
2010,
Pubmed
De Giorgi,
Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.
1996,
Pubmed
,
Echinobase
Ewing,
Base-calling of automated sequencer traces using phred. II. Error probabilities.
1998,
Pubmed
Ewing,
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
1998,
Pubmed
Fan,
Characterization of mitochondrial genome of sea cucumber Stichopus horrens: a novel gene arrangement in Holothuroidea.
2011,
Pubmed
,
Echinobase
Glover,
Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata.
2016,
Pubmed
,
Echinobase
Gordon,
Consed: a graphical tool for sequence finishing.
1998,
Pubmed
Hassanin,
Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae).
2009,
Pubmed
Larkin,
Clustal W and Clustal X version 2.0.
2007,
Pubmed
Laslett,
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.
2008,
Pubmed
Liu,
Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods.
2010,
Pubmed
Lowe,
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
1997,
Pubmed
Luo,
Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation.
2008,
Pubmed
Mah,
Global diversity and phylogeny of the Asteroidea (Echinodermata).
2012,
Pubmed
,
Echinobase
Maliarchuk,
[Adaptive evolution of the Homo mitochondrial genome].
2011,
Pubmed
Matsubara,
The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.
2005,
Pubmed
,
Echinobase
Matsubara,
Close relationship between Asterina and Solasteridae (Asteroidea) supported by both nuclear and mitochondrial gene molecular phylogenies.
2004,
Pubmed
,
Echinobase
Mishmar,
Natural selection shaped regional mtDNA variation in humans.
2003,
Pubmed
Perseke,
Evolution of mitochondrial gene orders in echinoderms.
2008,
Pubmed
,
Echinobase
Perseke,
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata.
2010,
Pubmed
,
Echinobase
Plazzi,
The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with conchifera.
2013,
Pubmed
Qureshi,
Two distinct, sequence-specific DNA-binding proteins interact independently with the major replication pause region of sea urchin mtDNA.
1993,
Pubmed
,
Echinobase
Ren,
Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia.
2010,
Pubmed
Scouras,
Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny.
2004,
Pubmed
,
Echinobase
Scouras,
The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: signature nucleotide bias and unique nad4L gene rearrangement within crinoids.
2006,
Pubmed
,
Echinobase
Shen,
A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.
2009,
Pubmed
Shen,
The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods.
2017,
Pubmed
Smith,
The phylogeny of echinoderm classes based on mitochondrial gene arrangements.
1993,
Pubmed
,
Echinobase
Smith,
Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus.
1990,
Pubmed
,
Echinobase
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Sun,
The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp.
2018,
Pubmed
Tamura,
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
2011,
Pubmed
Tang,
Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.
2014,
Pubmed
Tomasco,
The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection.
2011,
Pubmed
Wallace,
Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine.
2007,
Pubmed
Wolstenholme,
Animal mitochondrial DNA: structure and evolution.
1992,
Pubmed
Wyman,
Automatic annotation of organellar genomes with DOGMA.
2004,
Pubmed
Xu,
High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome.
2007,
Pubmed
Xu,
PAMLX: a graphical user interface for PAML.
2013,
Pubmed
Yang,
Bayes empirical bayes inference of amino acid sites under positive selection.
2005,
Pubmed
Yang,
The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite.
2008,
Pubmed
Yang,
PAML 4: phylogenetic analysis by maximum likelihood.
2007,
Pubmed
Yasuda,
Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus.
2006,
Pubmed
,
Echinobase
Yu,
Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation.
2011,
Pubmed
Zhang,
The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment.
2017,
Pubmed
Zhou,
Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds.
2014,
Pubmed
