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A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.

Shen X, Ma X, Ren J, Zhao F - BMC Genomics (2009)

Bottom Line: It shares many more similar features with the four known annelid and one echiuran mtDNAs.Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans).Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, PR China. shenthin@163.com

ABSTRACT

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum.

Results: The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups.

Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

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Putative secondary structures for 22 tRNA genes of the P. esculenta (Sipuncula: Phascolosomatidea). Watson-Crick and GT bonds are denoted by "-" and "+", respectively.
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Figure 3: Putative secondary structures for 22 tRNA genes of the P. esculenta (Sipuncula: Phascolosomatidea). Watson-Crick and GT bonds are denoted by "-" and "+", respectively.

Mentions: The P.esculenta mtDNA encodes 22 tRNA genes, each folding into a clover-leaf secondary structure (Figure 3) and ranging in size from 61 (trnC, trnM2 and trnH) to 72 (trnY) nucleotides. There are five cases in total where tRNA genes appear to overlap by one to six nucleotides (Table 1). Compared with a standard set of metazoan mt genomes, the sipunculid mitochondrial genome lacks trnR and has an extra trnM. The absence of tRNA gene(s) was found in some metazoan mitochondrial genomes [44,45]. Twenty two tRNA genes were identified on the basis of their respective anticodons and secondary structures. Gene sizes and anticodon nucleotides were congruent to those described for other metazoan species.


A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.

Shen X, Ma X, Ren J, Zhao F - BMC Genomics (2009)

Putative secondary structures for 22 tRNA genes of the P. esculenta (Sipuncula: Phascolosomatidea). Watson-Crick and GT bonds are denoted by "-" and "+", respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667193&req=5

Figure 3: Putative secondary structures for 22 tRNA genes of the P. esculenta (Sipuncula: Phascolosomatidea). Watson-Crick and GT bonds are denoted by "-" and "+", respectively.
Mentions: The P.esculenta mtDNA encodes 22 tRNA genes, each folding into a clover-leaf secondary structure (Figure 3) and ranging in size from 61 (trnC, trnM2 and trnH) to 72 (trnY) nucleotides. There are five cases in total where tRNA genes appear to overlap by one to six nucleotides (Table 1). Compared with a standard set of metazoan mt genomes, the sipunculid mitochondrial genome lacks trnR and has an extra trnM. The absence of tRNA gene(s) was found in some metazoan mitochondrial genomes [44,45]. Twenty two tRNA genes were identified on the basis of their respective anticodons and secondary structures. Gene sizes and anticodon nucleotides were congruent to those described for other metazoan species.

Bottom Line: It shares many more similar features with the four known annelid and one echiuran mtDNAs.Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans).Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, PR China. shenthin@163.com

ABSTRACT

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum.

Results: The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups.

Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

Show MeSH