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The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features.

Kilpert F, Podsiadlowski L - BMC Genomics (2006)

Bottom Line: It shows several changes in mitochondrial gene order compared to other crustacean species.The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods.This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Systematics and Evolution, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str, 1-3, D-14195 Berlin, Germany. fkil@zedat.fu-berlin.de

ABSTRACT

Background: Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines.

Results: The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4x 10 bp and 3x 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all.

Conclusion: Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

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Plots of the mitochondrial tRNAs found in Ligia oceanica. An additional nucleotide, probably deleted by RNA editing, is found in the anticodon loop of trnV (arrow).
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Figure 3: Plots of the mitochondrial tRNAs found in Ligia oceanica. An additional nucleotide, probably deleted by RNA editing, is found in the anticodon loop of trnV (arrow).

Mentions: Transfer-RNA genes are spread over the entire genome and are located on both strands (Fig. 1, Table 1). 14 of them were identified using tRNAscan-SE 1.21 [41]. The other seven tRNA genes (trnD, trnC, trnE, trnI, trnF, trnS1, trnW) were found by eye inspection of otherwise non-coding regions. Some of the putative secondary structures derive from the usual cloverleaf pattern (Fig. 3): tRNA-Cys and tRNA-Ser(AGY) lack the DHU-arm. The loss of this arm in tRNA-Ser(AGY) was also observed in many other arthropod species, among malacostracan crustaceans Pseudocarcinas gigas and Macrobrachium rosenbergi [42], Euphausia superba [43], Cherax destructor [33], Penaeus monodon [34], and Portunus trituberculatus [35]. In contrast to that, the derived structure of tRNA-Cys seems to be unique among malacostracan species studied so far. Transfer-RNA-Val and tRNA-Ile miss the TΨC-arm. Again these features are not seen in other malacostracan crustaceans.


The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features.

Kilpert F, Podsiadlowski L - BMC Genomics (2006)

Plots of the mitochondrial tRNAs found in Ligia oceanica. An additional nucleotide, probably deleted by RNA editing, is found in the anticodon loop of trnV (arrow).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590035&req=5

Figure 3: Plots of the mitochondrial tRNAs found in Ligia oceanica. An additional nucleotide, probably deleted by RNA editing, is found in the anticodon loop of trnV (arrow).
Mentions: Transfer-RNA genes are spread over the entire genome and are located on both strands (Fig. 1, Table 1). 14 of them were identified using tRNAscan-SE 1.21 [41]. The other seven tRNA genes (trnD, trnC, trnE, trnI, trnF, trnS1, trnW) were found by eye inspection of otherwise non-coding regions. Some of the putative secondary structures derive from the usual cloverleaf pattern (Fig. 3): tRNA-Cys and tRNA-Ser(AGY) lack the DHU-arm. The loss of this arm in tRNA-Ser(AGY) was also observed in many other arthropod species, among malacostracan crustaceans Pseudocarcinas gigas and Macrobrachium rosenbergi [42], Euphausia superba [43], Cherax destructor [33], Penaeus monodon [34], and Portunus trituberculatus [35]. In contrast to that, the derived structure of tRNA-Cys seems to be unique among malacostracan species studied so far. Transfer-RNA-Val and tRNA-Ile miss the TΨC-arm. Again these features are not seen in other malacostracan crustaceans.

Bottom Line: It shows several changes in mitochondrial gene order compared to other crustacean species.The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods.This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Systematics and Evolution, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str, 1-3, D-14195 Berlin, Germany. fkil@zedat.fu-berlin.de

ABSTRACT

Background: Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines.

Results: The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4x 10 bp and 3x 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all.

Conclusion: Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

Show MeSH