The complete mitochondrial genome of Cephalothrix simula (Iwata) (Nemertea: Palaeonemertea)

Chen, Hạixia; Sundberg, Per; Norenburg, Jon L.; Sun, Shichun

doi:10.1016/j.gene.2009.04.015

Cited by 15 publications

(13 citation statements)

References 67 publications

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“…Lengths of the two nemertean mitochondrial genomes are within the range of previously sequenced nemertean mtDNAs - 14558 bp in Paranemertes cf. peregrina to 16296 bp in Cephalothrix hongkongiensis [6]. Both of the newly sequenced mitochondrial genomes contain 37 genes, including 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs.…”

Section: Resultsmentioning

confidence: 99%

“…There are about 1275 described species [5] of nemerteans (ribbon worms, phylum Nemertea); these are mainly marine but terrestrial and freshwater species also are known. To date, complete mitochondrial genomes have been published for only three species in the phylum, Cephalothrix hongkongiensis (Palaeonemertea) [reported as Cephalothrix simula in [6]], Lineus viridis (Heteronemertea) [7], and Paranemertes cf. peregrina (Hoplonemertea)[8].…”

Section: Introductionmentioning

confidence: 99%

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A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea

et al. 2012

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BackgroundThe mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens.ResultsThe sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks.ConclusionThe two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea

et al. 2012

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“…mirabilis , Paranemertes cf. peregrina ) (e.g., [20], [21], [22], [23], [24]). Thus all three major lineages of nemerteans are represented and it is now possible to investigate codon usage bias and associated forces in phylum Nemertea.…”

Section: Introductionmentioning

confidence: 99%

Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)

et al. 2014

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The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

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“…Mitochondrial DNA (mtDNA) sequences have been extensively used as genetic markers for studying the taxonomy, systematics, and population genetics of animals due to their maternal inheritance, fast rate of evolutionary change, lack of recombination, and relatively conserved genome structures (Li et al 2008;Catanese et al 2010). To date, quite a number of complete mt genomes of metazoan species have been deposited in GenBank, mainly for Arthropoda, Mollusca, Platyhelminthes, Nematoda, and Chordata (Chen et al 2009). The class Trematoda currently contains about 18,000 nominal species, and the majority of trematode species can parasitize mammal animals including humans as definitive host (Olson et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Sequences and gene organization of the mitochondrial genomes of the liver flukes Opisthorchis viverrini and Clonorchis sinensis (Trematoda)

et al. 2011

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Opisthorchis viverrini and Clonorchis sinensis are important trematodes infecting humans and animals, belonging to the family Opisthorchiidae. In the present study, we sequenced the nearly complete mitochondrial (mt) DNA (mtDNA) sequences of O. viverrini from Laos, obtained the complete mtDNA sequences of C. sinensis from China and Korea, and revealed their gene annotations and genome organizations. The mtDNA sequences of O. viverrini, C. sinensis (China isolate), C. sinensis (Korea isolate) were 13,510, 13,879, and 13,877 bp in size, respectively. Each of the three mt genomes comprises 36 genes, consisting of 12 genes coding for proteins, two genes for rRNA, and 20 genes (O. viverrini) or 22 genes (C. sinensis) for tRNA. The gene content and arrangement are identical to that of Fasciola hepatica, and Paragonimus westermani, but distinct from Schistosoma spp. All genes are transcribed in the same direction and have a nucleotide composition high in T. The contents of A + T of the mt genomes were 59.39% for O. viverrini, 60.03% for C. sinensis (China isolate), and 59.99% for C. sinensis (Korea isolate). Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes, with three different computational algorithms [maximum parsimony, maximum likelihood, and Bayesian analysis], all revealed distinct groups with high statistical support, indicating that O. viverrini and C. sinensis represent sister taxa. These data provide additional novel mtDNA markers for studying the molecular epidemiology and population genetics of the two liver flukes and should have implications for the molecular diagnosis, prevention, and control of opisthorchiasis and clonorchiasis in humans and animals.

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The complete mitochondrial genome of Cephalothrix simula (Iwata) (Nemertea: Palaeonemertea)

Cited by 15 publications

References 67 publications

A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea

A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea

Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)

Sequences and gene organization of the mitochondrial genomes of the liver flukes Opisthorchis viverrini and Clonorchis sinensis (Trematoda)

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