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A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera)

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Abstract

We sequenced the complete mitochondrial genomes (mitogenomes) of three Hoplonemertea species, Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula, which are 14,616, 14,655 and 15,354 bp in length, respectively. Each of the three circular mitogenomes consists of 37 typical genes and some non-coding regions. The nucleotide composition of the coding strand is biased toward T, almost a half of total nucleotides in these mitogenomes. There are many poly-T tracts across these mitogenomes, which exhibit T-number variation within different clones of protein-coding genes, mainly resulting from false PCR amplification. The major non-coding regions have tandem repeat motifs and hairpin-like structures that may be associated with the initiation of replication or transcription. Data published to date for nemerteans show that Palaeonemertea species usually bear the largest mitogenomes, while representatives in the more recently derived Distromatonemertea clade bear the smallest ones; and that the gene arrangement of mitogenomes seems to be variable within the phylum Nemertea, but stable within either of Heteronemertea and Hoplonemertea.

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Abbreviations

mitogenome:

Mitochondrial genome

atp6 and atp8 :

ATP synthase subunits 6 and 8

cytb :

Cytochrome b

cox1-3 :

Cytochrome c oxidase subunits I–III

nad1–6 and nad4L :

NADH dehydrogenase subunits 1–6 and 4L

rrnL and rrnS :

The large and small subunits of ribosomal RNA

trnX :

Transfer RNA molecules with the one-letter code of corresponding amino acid

DHU loop:

Dihydrouridine loop

%INUC:

Percent of identical nucleotides

mNCR:

Major non-coding region

PCR:

Polymerase chain reaction

kb:

Kilobase

bp:

Base pair

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (30970333; 31172046). We are grateful to Professor Robert K. Okazaki and Mr. Hai-Lin Shen for helps in collecting specimens, to Dr. Wei Shi, Dr. Hai-Xia Chen and Miss Dong-Li Xu for assisting with the analyses.

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  1. Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China

    Wen-Yan Sun & Shi-Chun Sun

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  1. Wen-Yan Sun
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Correspondence to Shi-Chun Sun.

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11033_2014_3438_MOESM1_ESM.tif

Fig. S1. Number variation of poly-T tract within nad6 gene of Nipponnemertes punctatula. Boxes represent the correct number of T nucleotides to maintain a complete reading frame. Arrows point to T deletion/insertion. (TIFF 4806 kb)

11033_2014_3438_MOESM2_ESM.tif

Fig. S2. Alignment of the amino acids (represented by one letter) at the 3′ end of atp6 gene in nine nemertean species. The lowercase stands for the stop codon (TIFF 491 kb)

11033_2014_3438_MOESM3_ESM.tif

Fig. S3. Consensus secondary structure of trnS2 (AGN) for five hoplonemertean mitogenomes (Amphiporus formidabilis, Prosadenoporus spectaculum, Nipponnemertes punctatula, Paranemertes cf. peregrina and Nectonemertes cf. mirabilis). Capitalized bases are conserved in these species; lowercase bases are not compared (R = A/G, Y = C/T, W = A/U, K = G/U, N = A/U/G/C) (TIFF 184 kb)

11033_2014_3438_MOESM4_ESM.tif

Fig. S4. Major non-coding region of Nipponnemertes punctatula, showing the eight fragments that are predicted to form hairpin-like structures and the repeat (13 times) of the 11 bp motif GAAAGAAAAAA (highlighted). (TIFF 457 kb)

11033_2014_3438_MOESM5_ESM.tif

Fig. S5. Alignment of the gap region between cox1 and trnW in hoplonemerteans. The underlined nucleotides indicates conserved region among them. (TIFF 215 kb)

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Sun, WY., Sun, SC. A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera). Mol Biol Rep 41, 5681–5692 (2014). https://doi.org/10.1007/s11033-014-3438-5

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