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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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Putative secondary structures of the 22 tRNAs identified in the mitochondrial genome of the sea spider Achelia bituberculata.
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Figure 4: Putative secondary structures of the 22 tRNAs identified in the mitochondrial genome of the sea spider Achelia bituberculata.

Mentions: All 22 of the tRNAs typically found in metazoan mitochondrial genomes were identified in A. bituberculata. All these genes are located among protein- and/or rRNA-coding genes (Fig. 1 and Table 2). Twenty-two putative secondary structures were predicted from the tRNA gene sequences (Fig. 4). Most of the tRNAs are capable of forming the typical clover-leaf structure, with the exception of tRNAAla (which lacks both the DHU and TψC arms), tRNASer(AGN), tRNATyr and tRNAVal (which lacks only the DHU arm). The lengths of the TψC and DHU arms in the 18 tRNAs with a stable clover-leaf shape range from 4 to 12 bp, and the variable loops range in size from 4 to 5 bp. tRNASer(AGN) with an unpaired DHU arm has been reported in the mitochondrial genomes of a number of metazoa including the sea spider N. gracile [44], the centipede Scutigera coleoptrata [52], the jumping spider Habronattus oregonensis [47], the nematodes Caenorhabditis elegans and Ascaris suum [53] and the annelid Lumbricus terrestris [39]. The DHU arm of tRNAAla in N. gracile does not form a stable stem; however, the other two tRNAs, tRNATyr and tRNAVal, are folded into typical clover-leaf shapes [44].


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)

Putative secondary structures of the 22 tRNAs identified in the mitochondrial genome of the sea spider Achelia bituberculata.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Putative secondary structures of the 22 tRNAs identified in the mitochondrial genome of the sea spider Achelia bituberculata.
Mentions: All 22 of the tRNAs typically found in metazoan mitochondrial genomes were identified in A. bituberculata. All these genes are located among protein- and/or rRNA-coding genes (Fig. 1 and Table 2). Twenty-two putative secondary structures were predicted from the tRNA gene sequences (Fig. 4). Most of the tRNAs are capable of forming the typical clover-leaf structure, with the exception of tRNAAla (which lacks both the DHU and TψC arms), tRNASer(AGN), tRNATyr and tRNAVal (which lacks only the DHU arm). The lengths of the TψC and DHU arms in the 18 tRNAs with a stable clover-leaf shape range from 4 to 12 bp, and the variable loops range in size from 4 to 5 bp. tRNASer(AGN) with an unpaired DHU arm has been reported in the mitochondrial genomes of a number of metazoa including the sea spider N. gracile [44], the centipede Scutigera coleoptrata [52], the jumping spider Habronattus oregonensis [47], the nematodes Caenorhabditis elegans and Ascaris suum [53] and the annelid Lumbricus terrestris [39]. The DHU arm of tRNAAla in N. gracile does not form a stable stem; however, the other two tRNAs, tRNATyr and tRNAVal, are folded into typical clover-leaf shapes [44].

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