DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates (original) (raw)
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Mitochondrial COI-NC-COII sequences in talitrid amphipods (Crustacea)
Heredity, 2005
Mitochondrial (mt) sequences from cytochrome oxidase subunit I to the subunit II gene (COI, COII) were analysed in crustacean talitrid amphipods. Species of the genera Orchestia, Talitrus and Talorchestia from the Mediterranean-East Atlantic area were examined. The expected tRNALeu-UUR gene was not revealed between COI and COII. Instead, a short (35-48 bp) noncoding (NC) AT-rich (ca. 90%) region with putative stem loops was found. Here, we discuss briefly the NC region and explore its potential involvement in generating this novel rearrangement. The COI-NC-COII organization, as well as preliminary phylogenetic results, based on both COI-COII nucleotide and amino-acid sequence indicate monophyly of these talitrid taxa.
Universal cytochrome b primers facilitate intraspecific studies in molluscan taxa
Molecular marine biology and biotechnology, 1998
We describe the construction of amplification primers designed to target a portion of the mitochondrial cytochrome b locus in a variety of molluscan taxa. Combinations of two sets of primers successfully amplified cytochrome b from several species of gastropods, bivalves, and cephalopods. Sequence analysis of these amplified products revealed nucleotide diversity in small samples within several of these taxa. We discuss the utility of these primer sets for studies of intraspecific phylogeny in mollusks and potentially other invertebrates.
Cladistics, 2004
An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds.
Phylogeny of Cephalopods Inferred from Mitochondrial DNA Sequences
Molecular Phylogenetics and Evolution, 1997
Sequences of partial mitochondrial cytochrome oxidase III gene (533 bp) were obtained for 17 species of cephalopods, 14 decapods, 2 octopods, and 1 vampyromorph. This study aimed to: (1) compare partial COII and COIII amino acid sequences of three species of cephalopods with other invertebrates in terms of base composition and phylogenetic relationships. Cephalopod sequences are closer to Katharina tunicata sequences than to Mytilus edulis (marine bivalve) and Albinaria turrita (terrestrial gastropod); (2) investigate the phylogenetic relationships among cephalopods. Nucleotides as well as amino acid sequence variations of a COIII fragment were examined with parsimony and distance methods. Our data confirm the monophyly of the Decapoda and of each family. A high hierarchical rank for sepiolids, already suggested by other authors, appears justified. The order Sepioidea comprising five families should be abandoned, with Spirula being excluded. The surprising position of Idiosepius as the sister group of some oegopsids and not of sepioids or sepiolids is confirmed. Vampyroteuthis is the sister group of octopods. However, the data do not allow resolution of the phylogenetic relationships between the orders of Decapoda; consequently we suspect a rapid radiation. r 1997 Academic Press
Molecular Phylogenetics and Evolution, 2010
The ancestral genome composition in Onychophora (velvet worms) is unknown since only a single species of Peripatidae has been studied thus far, which shows a highly derived gene order with numerous translocated genes. Due to this lack of information from Onychophora, it is difficult to infer the ancestral mitochondrial gene arrangement patterns for Panarthropoda and Ecdysozoa. Hence, we analyzed the complete mitochondrial genome of the onychophoran Opisthopatus cinctipes, a representative of Peripatopsidae. Our data show that O. cinctipes possesses a highly conserved gene order, similar to that found in various arthropods. By comparing our results to those from different outgroups, we reconstruct the ancestral gene arrangement in Panarthropoda and Ecdysozoa. Our phylogenetic analysis of protein-coding gene sequences from 60 protostome species (including outgroups) provides some support for the sister group relationship of Onychophora and Arthropoda, which was not recovered by using a single species of Peripatidae, Epiperipatus biolleyi, in a previous study. A comparison of the strand-specific bias between onychophorans, arthropods, and a priapulid suggests that the peripatid E. biolleyi is less suitable for phylogenetic analyses of Ecdysozoa using mitochondrial genomic data than the peripatopsid O. cinctipes.
Molecular Phylogenetics and Evolution, 2010
The genome architecture and amino acid sequences of six new complete mitochondrial genomes were determined from representatives of Hemichordata (1), Ophiuroidea (3), Echinoidea (1) and Holothuroidea (1) and were analysed together with previously known sequences. Phylogenetic analyses recovered three lineages within echinoderms, Crinoidea, Ophiuroidea and a group comprising Holothuroidea, Echinoidea, and Asteroidea. In contrast to previous analyses of mitochondrial genomes the increased data set recovered the classical echinoderm phylogeny of Eleutherozoa and Echinozoa in Maximum Likelihood and Bayesian analyses using hemichordate out-group representatives. However, an inconsistent ramification appeared with vertebrate out-groups and in Maximum Parsimony and Neighbour Joining reconstructions.The basal (consensus) gene orders of all three lineages could be derived from a hypothetical ancestral crinoid gene order by one single rearrangement in each lineage. The genome architecture was highly conserved in Echinoidea, whereas the highest gene order differences and large amounts of unassigned sequences (UAS) were detected in Ophiuroidea, supporting a higher evolutionary rate than in any other echinoderm lineage. The variability in gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events.
Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids
BMC evolutionary biology, 2018
In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally ...