The first complete mitochondrial genome data of Hippocampus kuda originating from Malaysia

Abstract The mitochondrial genome is highly informative for evolutionary analysis of organism lineages and phylogenetic studies. The availability of robust primers for amplifying complete mitochondrial genomes is a crucial step in current mitogenome studies. However, organism specific characteristics such as variable transition to transversion substitution ratios seen in some groups pose challenges for the development of universal, or at least broadly applicable, primer pairs for this purpose. This study reports on a strategy of primer design and optimization (PDO) where regions of known mtDNA genescan be used for choosing primers for amplification, sequencing and assembly of entire mitochondrial genomes of several closely-related species. In brief, taking advantage of the circular organization of mtDNA, primers are first designed for amplification of “long” products using the 5’ region of one conserved gene and a 3’region from another conserved gene. Additional primers are then used to amplify “short” regions to fill in gaps to allow for complete assembly of the genome. We show how we were able to use this approach to successfully amplify entire mitochondrial genomes from a non-human primate species (Semnopithecus hypoleucos), and also how this provided data useful for annotation of the assembled genome data.

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The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order

Genome ◽

10.1139/g09-023 ◽

2009 ◽

Vol 52 (5) ◽

pp. 456-466 ◽

Cited By ~ 13

Author(s):

Kathrin Fahrein ◽

Susan E. Masta ◽

Lars Podsiadlowski

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Large Data ◽

Sister Group ◽

Mitochondrial Genomes ◽

Data Set ◽

Weak Support ◽

Genome Data

Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning arachnid mitochondrial genomics, we present the first two complete mitochondrial genomes from Amblypygi. Both genomes were found to be typical circular duplex DNA molecules with all 37 genes usually present in bilaterian mitochondrial genomes. In both species, gene order is identical to that of Limulus polyphemus (Xiphosura), which is assumed to reflect the putative arthropod ground pattern. All tRNA gene sequences have the potential to fold into structures that are typical of metazoan mitochondrial tRNAs, except for tRNA-Ala, which lacks the D arm in both amblypygids, suggesting the loss of this feature early in amblypygid evolution. Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi.

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Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning

ZooKeys ◽

10.3897/zookeys.793.28977 ◽

2018 ◽

Vol 793 ◽

pp. 1-14

Author(s):

Wentao Niu ◽

Shuangen Yu ◽

Peng Tian ◽

Jiaguang Xiao

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Molecular Data ◽

Start Codon ◽

Gene Arrangement ◽

Protein Coding ◽

Genome Data ◽

Mitogenome Sequence ◽

Complete Mitogenome ◽

First Time

Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coralEchinophylliaaspera(Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows thatE.asperaclustered closely withSclerophylliamaxima(Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome ofE.asperaprovides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

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First complete mitochondrial genome data from ancient South American camelids - The mystery of the chilihueques from Isla Mocha (Chile)

Scientific Reports ◽

10.1038/srep38708 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 4

Author(s):

Michael Westbury ◽

Stefan Prost ◽

Andrea Seelenfreund ◽

José-Miguel Ramírez ◽

Elizabeth A. Matisoo-Smith ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

South American ◽

South American Camelids ◽

Genome Data

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Complete mitochondrial genome of Cultellus attenuatus and its phylogenetic implications

10.21203/rs.3.rs-868770/v2 ◽

2021 ◽

Author(s):

Haikun Li ◽

Ruihai Yu ◽

Peizhen Ma ◽

Chunhua Li

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genes ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Transfer Rnas ◽

Genome Data ◽

Phylogenetic Implications ◽

Solen Grandis ◽

Relationship Of

Abstract The complete mitochondrial genome of Cultellus attenuates, a new aquaculture species, was sequenced and compared with mitogenomes from seven species of Heterodonta bivalve mollusk in GenBank. The mitochondrial genome of C. attenuatus is 16888 bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and all genes are encoded on the same strand. In comparison with C. attenuates, the mitochondrial genes of Sinonovacula constricta from the same family were not rearranged, but those of six other species from different families were rearranged to different degrees. The largest noncoding region of C. attenuatus is 1173 bp in length and has an A + T content of 68.24%, located between nad2 and trnK. The results of phylogenetic analysis show that C. attenuates and S. constricta belonging to Cultellidae cluster into one branch while two species of Solenidae (Solen grandis and Solen strictus) cluster as their sister taxa. In conclusion, we used the mitochondrial genome data to demonstrate the closest relationship between C. attenuatus and S. constricta in Heterodonta. These data not only contribute to the understanding of the phylogenetic relationship of Heterodonta but also serve as a resource for the development of genetic markers in aquaculture.

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