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The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement.

Park SJ, Lee YS, Hwang UW - BMC Genomics (2007)

Bottom Line: This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression.Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected.However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea. shinju@knu.ac.kr

ABSTRACT

Background: The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.

Results: The complete mitochondrial genome (15,474 bp) of a sea spider (Achelia bituberculata) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile) may be closely related to the clade of Acari and Araneae.

Conclusion: The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae) and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like), but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

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Primary and secondary structures of the control region in the mitochondrial genome of the sea spider Achelia bituberculata. (A) The nucleotide sequence alignment of three repeat units observed in the control region of the mitochondrial genome of A. bituberculata. The lengths of the first and second repeat units are 315 bp. The 3'-end of the third repeat is truncated by 33 bp, resulting in a shorter repeat unit (282 bp). A red box indicates a single nucleotide difference observed in the third repeat unit. Dashes indicate truncated nucleotide sequences absent from the third repeat unit. (B) Putative secondary structure predicted from a large repeat unit (315 bp). An arrow marks the position truncated in the third repeat unit. An 'A' in parentheses indicates that a 'G' appears in the first and second repeat units, but an 'A' appears in the third repeat unit in position 3057 [GenBank: AY457170].
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Figure 5: Primary and secondary structures of the control region in the mitochondrial genome of the sea spider Achelia bituberculata. (A) The nucleotide sequence alignment of three repeat units observed in the control region of the mitochondrial genome of A. bituberculata. The lengths of the first and second repeat units are 315 bp. The 3'-end of the third repeat is truncated by 33 bp, resulting in a shorter repeat unit (282 bp). A red box indicates a single nucleotide difference observed in the third repeat unit. Dashes indicate truncated nucleotide sequences absent from the third repeat unit. (B) Putative secondary structure predicted from a large repeat unit (315 bp). An arrow marks the position truncated in the third repeat unit. An 'A' in parentheses indicates that a 'G' appears in the first and second repeat units, but an 'A' appears in the third repeat unit in position 3057 [GenBank: AY457170].

Mentions: A large noncoding region [= a plausible control region (CR); 977 bp] is found between trnQ and trnI. It includes three tandem repeats, the first and second of which are completely identical in length (315 bp) and sequence (Fig. 5A). However, the third repeat (282 bp) is 33 bp shorter than the other two at the 3'-end, and one nucleotide is different in the 315-bp repeat (Fig. 5A). The repeats have unique stem and loop structures that may play key roles in controlling the replication and transcription of the mitochondrial genome (Fig. 5B). The A+T content of the CR is 79%, which is similar to those of most chelicerates (Table 1).


The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement.

Park SJ, Lee YS, Hwang UW - BMC Genomics (2007)

Primary and secondary structures of the control region in the mitochondrial genome of the sea spider Achelia bituberculata. (A) The nucleotide sequence alignment of three repeat units observed in the control region of the mitochondrial genome of A. bituberculata. The lengths of the first and second repeat units are 315 bp. The 3'-end of the third repeat is truncated by 33 bp, resulting in a shorter repeat unit (282 bp). A red box indicates a single nucleotide difference observed in the third repeat unit. Dashes indicate truncated nucleotide sequences absent from the third repeat unit. (B) Putative secondary structure predicted from a large repeat unit (315 bp). An arrow marks the position truncated in the third repeat unit. An 'A' in parentheses indicates that a 'G' appears in the first and second repeat units, but an 'A' appears in the third repeat unit in position 3057 [GenBank: AY457170].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194727&req=5

Figure 5: Primary and secondary structures of the control region in the mitochondrial genome of the sea spider Achelia bituberculata. (A) The nucleotide sequence alignment of three repeat units observed in the control region of the mitochondrial genome of A. bituberculata. The lengths of the first and second repeat units are 315 bp. The 3'-end of the third repeat is truncated by 33 bp, resulting in a shorter repeat unit (282 bp). A red box indicates a single nucleotide difference observed in the third repeat unit. Dashes indicate truncated nucleotide sequences absent from the third repeat unit. (B) Putative secondary structure predicted from a large repeat unit (315 bp). An arrow marks the position truncated in the third repeat unit. An 'A' in parentheses indicates that a 'G' appears in the first and second repeat units, but an 'A' appears in the third repeat unit in position 3057 [GenBank: AY457170].
Mentions: A large noncoding region [= a plausible control region (CR); 977 bp] is found between trnQ and trnI. It includes three tandem repeats, the first and second of which are completely identical in length (315 bp) and sequence (Fig. 5A). However, the third repeat (282 bp) is 33 bp shorter than the other two at the 3'-end, and one nucleotide is different in the 315-bp repeat (Fig. 5A). The repeats have unique stem and loop structures that may play key roles in controlling the replication and transcription of the mitochondrial genome (Fig. 5B). The A+T content of the CR is 79%, which is similar to those of most chelicerates (Table 1).

Bottom Line: This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression.Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected.However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea. shinju@knu.ac.kr

ABSTRACT

Background: The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.

Results: The complete mitochondrial genome (15,474 bp) of a sea spider (Achelia bituberculata) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile) may be closely related to the clade of Acari and Araneae.

Conclusion: The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae) and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like), but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

Show MeSH
Related in: MedlinePlus