pmc.ncbi.nlm.nih.gov

Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei

. Author manuscript; available in PMC: 2014 May 18.

Published in final edited form as: Mol Phylogenet Evol. 2011 Dec 21;63(1):203–207. doi: 10.1016/j.ympev.2011.12.009

Abstract

Ctenophores are one of the most basally branching lineages of metazoans with the largest mitochondrial organelles in the animal kingdom. We sequenced the mitochondrial (mtDNA) genome from the Pacific cidipid ctenophore, Pleurobrachia bachei. The circular mitochondrial genome is 11,016 nts, with only 12 genes, and one of the smallest metazoan mtDNA genomes recorded. The protein coding genes are intronless cox1-3, cob, nad1, 3, 4, 4L and 5. The nad2 and 6 genes are represented as short fragments whereas the atp6 gene was found in the nuclear genome. Only the large ribosomal RNA subunit and 2 tRNAs were present with possibly the small subunit unidentifiable due to extensive fragmentation. The observed unique features of this mitochondrial genome suggest that nuclear and mitochondrial genomes have evolved at very different rates. This reduced mtDNA genome sharply contrasts with the very large sizes of mtDNA found in other basal metazoans including Porifera (sponges), and Placozoa (Trichoplax).

Keywords: mitochondrial genome, ctenophore, basal metazoan, gene loss

1. Introduction

Comb jellies, or ctenophores, are holoplanktonic predators, representatives of one of the most basally branching lineages of metazoans, and critical for our understanding of early animal evolution. In metazoans, there are five basal taxa, including ctenophores (Ctenophora), sponges (Porifera), cnidarians (polyps and medusas), placozoans (Placozoa, Trichoplax), and bilaterians. Relationships among these taxa are presently unclear, but may be further illuminated by genomic studies. The phylogenetic position of Ctenophora is still highly controversial (Hejnol et al., 2009; Philippe et al., 2009) and very little is known about their molecular organization. However, Ctenophora is the only major non-bilaterian lineage for which genomic studies are lacking.

Ctenophores are the largest animals to propel themselves by cilia. Their elongated cells that support these cilia of the comb rows have the largest mitochondrial organelles in the animal kingdom, reaching up to 8 μm in diameter (Horridge, 1964). Here, we report the first sequencing of the mitochondrial (mtDNA) genome in ctenophores from the Pacific cidipid, Pleurobrachia bachei A. Agassiz, 1860. Surprisingly, Pleurobrachia has one of the smallest and most derived animal mitochondrial genomes, suggesting an extensive degree of evolution in this ancestral lineage.

2. Materials and Methods

2.1 Animal collection and molecular work

Animals were collected from the dock at Friday Harbor Laboratories (Friday Harbor, WA) in spring-summer 2008-2010. They were maintained for up to one week in running sea water at 10°C or filtered sea water at 4°C until further use. All animals were examined for exo-parasites then washed three times in twice filtered (0.2 μm) sea water. Animals were anesthetized by incubation in isotonic MgCl2 (337mM). Both RNA and DNA were isolated for sequencing. Genomic DNA was extracted with a genomic tip 100 (Cat# 10243, Qiagen) and buffer set (Cat #19060, Qiagen) according to the manufacture’s recommendations. Incubation of between 1-10 animals was with lysis buffer and proteinase K at 50°C for 10 min followed with RNase treatment. We finally eluted the gDNA in 100 ul of MQ water. This gDNA was then used for PCR amplification or library construction for high through-put genomic sequencing. Over 20 × coverage of the genome with 454 sequencing was obtained and an assembly was constructed from this sequencing data.

Initially, sequences with high similarity to cox1 and cob genes were identified by BlastP in our original 454 transcriptome datasets. Next, specific primers for these predicted mitochondrial genes were designed and gDNA was amplified and sequenced. Then primers were designed to walk along the whole mitochondrial genome. Sequencing was finished when the sequence circularized. The large-scale genomic 454 sequencing validated the mitochondrial genome with more than 20 × physical coverage, and a single scaffold representing the entire mitochondrial sequence.

Analysis of nucleotide composition was performed with in-house perl scripts. Predictions for tRNAs were performed with tRNAScan-SE (Lowe and Eddy, 1997; Schattner et al., 2005), ARWEN http://130.235.46.10/ARWEN/ and MITOS, a free web server at http://mitos.bioinf.uni-leipzig.de.

2.2 Phylogenomic analyses

Mitochondrial genome processing

Complete mitochondrial genomes were downloaded from NCBI and amino acid sequences for the 13 protein-coding genes found in most metazoan mitochondrial genomes and were parsed into individual fasta files using the mitobank Perl script. All protein-coding genes from the P. bachei mitochondrion were used in the analysis.

Orthology assignment and dataset assembly

All OGs were then trimmed using gblocks (b1 = half the number of sequences in alignment plus one, b2 = b1, b3 = 8, b4 = 2, b5 = h) to remove regions with ambiguous the alignment or little to no phylogenetic signal. A final data matrix of all 13 protein-coding genes was assembled using FASconCAT.

Phylogenetic analyses

Phylogenetic analyses were conducted using ML in RAxML 7.2.7 and BI in PhyloBayes 2.3 (Fig. 1S on the Alabama Supercomputer Authority Dense Memory Cluster (http://www.asc.edu/). For ML analyses, the CAT + WAG +F model was used. Topological robustness (i.e., nodal support) for all ML analyses was assessed with 100 replicates of nonparametric bootstrapping. For the BI analysis, the CAT model was employed to account for site-specific rate heterogeneity. BI analyses were conducted with five parallel chains run for 15,000 cycles each, with the first 5,000 trees discarded as burn-in. A 50% majority rule consensus tree was computed from the remaining 10,000 trees from each chain. Topological robustness was assessed using posterior probabilities. Species, abbreviations and their accession numbers used in phylogenetic analysis can be found in Supplementary Material 1S.

3. Results

3.1 Features of the mitochondrial genome from P. bachei

Using standard molecular biology techniques complimented with 454 and Illumina sequencing technology, we sequenced the complete mitochondrial genome of P. bachei at >20 X coverage. To verify the assembled mtDNA genome, we then PCR amplified, cloned and Sanger sequenced the mtDNA genome to validate the overall assembly as a single scaffold. The circular mtDNA genome of Pleurobrachia (Acc # JN392469) is 11,016 nts in length (Fig. 1). Thus, P. bachei has the most compact metazoan mitochondrial genome ever reported.

Fig. 1. Genomic map of the P. bachei mitochondrial genome.

Fig. 1

Gray areas are noncoding regions, dotted lines are tRNAs. Gene and gene product abbreviations are the following; cox 1-3 cytochrome c oxidase subunits, nad 1,3,4,4L and 5 NADH dehydrogenase subunits, cob cytochrome b apoprotein, lrRNA large ribosomal RNA. The light pink bars represent the areas were the highly fragmented nad2 and 6 sequences are located.

This compact mtDNA genome is comprised of just 9 intronless protein-coding genes (versus 13 protein coding genes in a majority of animals (Chan, 2006)), 1 large ribosomal RNA gene and 2 tRNA genes (Fig. 1 and Table 1). The nine protein coding genes encode for the following: cytochrome oxidase subunit I, cytochrome oxidase subunit II, cytochrome oxidase subunit III, NADH dehydrogenase subunit 1, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4, NADH dehydrogenase subunit 4L, NADH dehydrogenase subunit 5 and cytochrome b. All use AUG as a start codon except for NAD1, which uses AUU; and all protein coding genes use UAA as a stop codon. The nad2 and 6 genes are found as incomplete fragments (<50nt identifiable fragments) in the mitochondrial genome and have not been identified in the nuclear genome either. Both nad2 and 6 genes have low homology to other mitochondrial proteins. Areas where fragments were identified are marked in light pink Fig. 1.

Table 1.

Genes identified in the mitochondrial genome of P. bachei.

Gene Position Stand Start Stop Length (bp) Coding (aa) UGA
cox 1 1-1464 + ATG TAA 1464 484 (4) G, T, A
cox 2 1585-2166 + ATG TAA 582 193 (1) A
tRNA-G (ACC) 2483-2544 - 62
tRNA-P (TGG) 3220-3277 + 58
nad4L 3344-3523 + ATG TAA 180 60 (1) I
lrRNA 3524-3940 + 416
cox 3 3979-4719 + ATG TAA 741 246 (3) S, T
nad4 5590-6837 + ATG TAA 1248 415 (2) G, L
cob 7035-8081 + ATG TAA 1047 348 (6) S, E, P S, G, L
nad5 8101-9597 + ATG TAA 1497 498 (11) I, G, T, S, M, P
nad1 9588-10436 + ATT TAA 849 282 (3) L, V
nad3 10728-10928 + ATG TAA 210 70 0

No atpase subunits 6, 8 or 9 were detected in the P. bachei mt genome. However, we identified and cloned a complete atp6 gene from the nuclear genome and found that it contains four introns (Table 1S and see alignments in 3S Supplementary Material). The mitochondrial large ribosomal subunit is small in size and highly derived, whereas the small ribosomal subunit is not detected, possibly due to extensive unidentifiable fragmentation, or is not present.

There are 4 canonical codons reported for other animal mt genomes that were not used in P. bachei’s mtDNA -- Arg; CGA, Arg; CGG, Pro; CCG and Stop; UAG (see Table 2S in Supplementary Material, and analysis using the Invertebrate Mitochondrial Code). In most metazoan mitochondrial genomes the UGA codon is a Tryptophan residue (Trp), however the UGA codon is undetermined in P. bachei’s mitochondrial genome. Based on alignments with other conserved proteins, UGA has the potential to encode different amino acids (Table 1 and Table 3S in Supplementary Material).

Overall nucleotide composition is 23% G+C. All genes are transcribed unidirectionally, except for the tRNA-G, from the coding strand, which has an asymmetrical nucleotide composition of 52.3% T, 24.4% A, 13.1% C and 10.2 % G. The genome composition is 76% coding (protein, rRNA and tRNA) and 24% non-coding. No other open reading frames (ORF) were identified.

3.2 Ctenophore mitochondrial genome reflects high rate of nucleotide substitution

Phylogenomic analysis of mt genomes was performed with 94 species from all major animal clades whose conserved protein coding sequences were concatenated (species used, accession numbers for mtDNA genomes and methodological details are described in Supplementary Material 1S). Fig. 2 depicts the tree obtained by maximum likelihood (ML) in RAxML 7.2.7 (see additional trees Figs. 1S and 2S in the Supplementary Material). Phylogenetic placement of P. bachei is problematic because of the elevated rate of base substitution (i.e., long-branch attraction). Indeed, this particular position looks to be an artifact of the long-branch attraction. Evident gene loss plus no unknown ORF found in P. bachei mtDNA further support that the mt genome in the ctenophore lineage has been subject to rapid evolution compared to other animals sequenced so far.

Fig 2. Phylogenomic analysis of concatenated proteins in animal mitochondrial genomes.

Fig 2

For methods see 2S Supplementary Material, which also includes a list of all accession numbers and abbreviations for each species used in the tree. Only major branches show bootstrap support. This tree is also shown in Fig. 1S and Fig. 2S as a cladograms. The ctenophore mt genome is likely a subject of rapid evolution and the position of Pleurobrachia in the tree might reflect the long-branch attraction.

4. Discussion

4.1 Mitochondrial genome comparison reveals multiple gene loss

The recent advent of convenient, cheaper and fast sequencing capabilities has facilitated progress in the field, with 2406 animal mt genomes having been sequenced by Sept 2011. The majority of animals sequenced so far have a ‘typical’ 15, 000-18,000 nt mtDNA genome with 37 genes: 13 protein subunits in the respiratory complexes I, III, IV and V, 22 mitochondrial tRNA (20 standard amino acids, plus an extra gene for leucine and serine), and 2 rRNA (Chan, 2006). Most sequenced mtDNA genomes are from bilaterian animals (especially vertebrates and arthropods), leaving the basal metazoans under represented. There are 5 mt genomes from Placozoans (likely representing different lineages of Trichoplax), 42 mt genomes from sponges and 45 mt genomes from Cnidaria. Thus, Ctenophora is the major basal metazoan lineage lacking any information about mtDNA genomes. Here we report one of the smallest, 11,016 nts, of all metazoan mtDNA genomes from the ctenophore Pleurobrachia bachei.

The P. bachei gene complement described here contrasts even with all other basal metazoan genomes that typically have larger sizes and more genes than bilaterial animals (see Table 2). Indeed, the largest mtDNA genome has been reported in the placozoan, Trichoplax adhaerens, at 43,079 nts and 47 genes (Dellaporta et al., 2006; Signorovitch et al., 2007); representatives of choanoflagellates, sister group to Metazoa, and other unicellular Opistokonta (e.g. Capsaspora) and fungi possess even larger genomes (Burger et al., 2003; Burger and Lang, 2003; Lang et al., 2002). Therefore, there is a recognized trend for significant mitochondrion gene loss in the course of animal evolution and a reduction of the mt genome size compared to a common ancestor of all metazoans. The fact that P. bachei has the most compact mtDNA genome can be interpreted as a highly derived feature.

Table 2.

Summary of mtDNA genome features across various Metazoa and the Choanoflagellate Monosiga.

Phylum Species* Accession Number mtDNA genome Size (nt) % Coding + RNA # Protein Coding genes # tRNA/rRNA nad gene loss Presence of:
atp6 atp8 atp9 Ribosomal Proteins (others)
Choanoflagellata Monosiga brevicollis NC_004309 76,568 41% 32 25/2 + + + +
Ctenophora Pleurobrachia bachei JN392469 11,016 71% 9 2/1 nad2,6 - - - -
Porifera Lubomirskia baicalensis NC_013760 28,958 43% 14 25/2 + + + -
Oscarella carmela NC_009090 20,327 65% 15 27/2 + + + mttB
Plakina trilopha NC_014852 20,427 60% 12 3/2 nad4L + + - -
Ircinia strobilina NC_013662 16,414 73% 14 2/2 + + + -
Cnidaria Ephydatia muelleri NC_010202 23,929 52% 14 25/2 + + + -
Nematostella sp. NC_008164 16,389 72% 17 2/2 + + - -
Astrangia sp. NC_008161 14,853 77% 17 2/2 + + - -
Placozoa Trichoplax. adhaerens NC_008151 43,079 27% 20 24/3 + - - 8 Hypothetical
Placozoan sp.BZ2423 NC_008834 36,699 46% 14 24/3 + - - 2 Hypothetical
Placozoan sp.BZ10101 NC_008832 32,661 45% 14 24/3 + - - 2 Hypothetical
Cheatognatha Sagitta enflata NC_013814 12,631 73% 11 1/2 - - - -
Mollusca Aplysia californica NC_005827 14,117 76% 13 22/2 + + - -
Mytilus edulis NC_006161 16,740 66% 12 23/2 + + - -
Chordata Homo sapiens NC_012920 16,569 68% 13 22/2 + + - -
Polypedates megacephalus NC_006408 16,702 56% 11 22/2 nad5 + - - -

The mtDNA genome of P. bachei encodes only 9 protein coding genes - the smallest complement of protein coding genes found in any metazoan mitochondrial genome to date. A complete atp6 gene is present in the nuclear genome, suggesting secondary relocation of its function to the nucleus. However, it is not clear if the two fragmented genes nad2 and 6, as well as the short nad3 and 4L, encode for functional proteins. There are no recognized complements for these nad genes, or the missing mtDNA atp8 gene, in the nuclear genome.

On a smaller scale, trends of gene loss within mtDNA can be observed in other animal groups (Table 2). For example in sponges, Plakina trilopha’s mitochondrial genome is missing the nad4L gene (Gazave et al., 2010) and the Sympagella nux mtDNA genome lost both atp8 and nad6 (Haen et al., 2007). In metazoans, atp8 is the smallest mitochondrial encoded protein, being only 50-65 amino acid residues long, and only about a half dozen of these amino acid residues are well conserved across animal mtDNAs. Among the animal groups that have been sampled, atp8 has been independently lost from the mtDNA genomes in some bivalve molluscs (Ren et al., 2010) but is found in others (e.g. in Mytilus see (Breton et al., 2010); (Smietanka et al., 2010)), secernentean nematodes (Lavrov and Brown, 2001), and platyhelminths (Le et al., 2000)). All 5 species of chaetognaths studied so far have also lost both their atp6 and 8 genes (Faure and Casanova, 2006; Helfenbein et al., 2004; Miyamoto et al., 2010). Interestingly, even a very conservative organization of mtDNA genomes in land vertebrates can be subject to extensive gene loss, as reported for certain amphibians. For example, the mtDNA genome of the tree frog, Polypedates megacephalus, lost both atp8 and nad5 genes (Zhang et al., 2005a; Zhang et al., 2005b), see details in Table 2. Of course, there is a possibility of extensive mitochondrial RNA editing for nad2, nad3, nad4L, and nad6 (Vanfleteren and Vierstraete, 1999), resulting in the lack of the recognized sequences. Complete genome sequencing is required to identify these components in the nucleus. However, all currently available 454 data suggest that this possibility is unlikely.

The dynamic evolutionary nature of mt genomes is also supported by their high variability of total genes and tRNA genes across Metazoa. For example porifera’s gene content ranges from 44 genes to 18 genes. Gene loss particularly for the tRNA genes appears to be common in cnidarians such as the sea anemone, Nematostella, as well as Sarcophyton glaucum, Renilla kolikeri, and Metridium senile which contain only 2 tRNA genes (Medina et al., 2006).

The presence of only 2 tRNAs and 1 rDNA in P. bachei’s mtDNA genome suggest gene loss was not restricted to protein coding genes. By comparison, chaetognaths lost all but one of their tRNA genes (Faure and Casanova, 2006; Helfenbein et al., 2004; Miyamoto et al., 2010). Interestingly, some unicellular eukaryotes such as apicomplexans and trypanosomatids encode no tRNAs in their mtDNA genomes. Plants still preserve some tRNAs from a common eukaryote ancestor, and they import multiple tRNAs from the cytosol into their mitochondria (see review (Schneider, 1994)). Similar mechanisms might operate in the ctenophore P. bachei to support mitochondrial functions.

In summary, further transcriptome and genomic information from P. bachei and related species is needed to reconstruct the unique evolutionary history and functional adaptations in the mitochondrion of ctenophores. As recently shown for human mitochondria, direct transcriptional profiling is vital to decipher and validate the functional role of unconserved RNA or fragmented protein coding genes (Mercer et al., 2011). It is possible that some ‘missing’ components of the Pleurobrachia mt genome complement (e.g. srRNA) are highly fragmented beyond recognition and/or functionally not required. At this moment we posit that the RNA/protein content of the mtDNA genome in ctenophores is the smallest among animals and therefore dependent on import from the nuclear genome.

Note in Proof

While this paper was under review the Mnemiopsis leidyi mitochondrial genome was published (Pett et al., 2011). The findings in these two studies are in close accordance. The just released Mnemiopsis mt genome is similar to the Pleurobrachia genome (Both mt genomes are extremely AT rich and have high rates of substitution) but has several differences that can be summarized as follows. (i) the Pleurobrachia genome still has 2 tRNA’s, where as there are none in the Mnemiosis mt genome; (ii) Mnemiopsis has a small and large mt rRNA, whereas the small mt rRNA was unidentifiable in Pleurobrachia; (iii) nad2 is recognized as incomplete fragment in Pleurobrachia but is present as a full coding sequence in Mnemiopsis; (iv) there is a possibility that atp6 has been transferred to the nuclear genome prior to the divergence of both species but additional analysis of other ctenophore mt genomes would be desirable to resolve the reported unique features of their organization and evolution.

Supplementary Material

01

Acknowledgments

We would like to thank Friday Harbor Labs (University of Washington) for support of animal collection; Jim Netherton and two anonymous reviewers for their thoughtful and valuable comments on the manuscript. We would also like to acknowledge Dr. Gertraud Burger for her initial advice and help in analysis of the tRNAs as well as comments on an earlier version of manuscript. This work is supported by NIH grants 1RO1NS060762, 1R01GM097502, R21RR025699, 5R21DA030118, McKnight Brain Research Foundation, and NSF-0744649.

Abbreviations

mtDNA genome

Mitochondrial genome

Footnotes

Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

References

  1. Breton S, Stewart DT, Hoeh WR. Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): identification of the “missing” ATPase 8 gene. Mar Genomics. 2010;3:11–18. doi: 10.1016/j.margen.2010.01.001. [DOI] [PubMed] [Google Scholar]
  2. Burger G, Forget L, Zhu Y, Gray MW, Lang BF. Unique mitochondrial genome architecture in unicellular relatives of animals. Proc Natl Acad Sci U S A. 2003;100:892–897. doi: 10.1073/pnas.0336115100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burger G, Lang BF. Parallels in genome evolution in mitochondria and bacterial symbionts. IUBMB Life. 2003;55:205–212. doi: 10.1080/1521654031000137380. [DOI] [PubMed] [Google Scholar]
  4. Chan DC. Mitochondria: dynamic organelles in disease, aging, and development. Cell. 2006;125:1241–1252. doi: 10.1016/j.cell.2006.06.010. [DOI] [PubMed] [Google Scholar]
  5. Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA, Buss LW, Schierwater B. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci U S A. 2006;103:8751–8756. doi: 10.1073/pnas.0602076103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Faure E, Casanova JP. Comparison of chaetognath mitochondrial genomes and phylogenetical implications. Mitochondrion. 2006;6:258–262. doi: 10.1016/j.mito.2006.07.004. [DOI] [PubMed] [Google Scholar]
  7. Gazave E, Lapebie P, Renard E, Vacelet J, Rocher C, Ereskovsky AV, Lavrov DV, Borchiellini C. Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha) PLoS One. 2010;5:e14290. doi: 10.1371/journal.pone.0014290. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Haen KM, Lang BF, Pomponi SA, Lavrov DV. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? Mol Biol Evol. 2007;24:1518–1527. doi: 10.1093/molbev/msm070. [DOI] [PubMed] [Google Scholar]
  9. Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguna J, Bailly X, Jondelius U, Wiens M, Muller WE, Seaver E, Wheeler WC, Martindale MQ, Giribet G, Dunn CW. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci. 2009;276:4261–4270. doi: 10.1098/rspb.2009.0896. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Helfenbein KG, Fourcade HM, Vanjani RG, Boore JL. The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes. Proc Natl Acad Sci U S A. 2004;101:10639–10643. doi: 10.1073/pnas.0400941101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Horridge GA. The Giant Mitochondria of Ctenophore Comb-Plates. Quarterly Journal of Microscopical Science. 1964;s3:301–310. [Google Scholar]
  12. Lang BF, O’Kelly C, Nerad T, Gray MW, Burger G. The closest unicellular relatives of animals. Curr Biol. 2002;12:1773–1778. doi: 10.1016/s0960-9822(02)01187-9. [DOI] [PubMed] [Google Scholar]
  13. Lavrov DV, Brown WM. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. Genetics. 2001;157:621–637. doi: 10.1093/genetics/157.2.621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Le TH, Blair D, Agatsuma T, Humair PF, Campbell NJ, Iwagami M, Littlewood DT, Peacock B, Johnston DA, Bartley J, Rollinson D, Herniou EA, Zarlenga DS, McManus DP. Phylogenies inferred from mitochondrial gene orders-a cautionary tale from the parasitic flatworms. Mol Biol Evol. 2000;17:1123–1125. doi: 10.1093/oxfordjournals.molbev.a026393. [DOI] [PubMed] [Google Scholar]
  15. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–964. doi: 10.1093/nar/25.5.955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A. 2006;103:9096–9100. doi: 10.1073/pnas.0602444103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS. The human mitochondrial transcriptome. Cell. 2011;146:645–658. doi: 10.1016/j.cell.2011.06.051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Miyamoto H, Machida RJ, Nishida S. Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata. Comp Biochem Physiol Part D Genomics Proteomics. 2010;5:65–72. doi: 10.1016/j.cbd.2009.11.002. [DOI] [PubMed] [Google Scholar]
  19. Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD, Lavrov DV. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. Mitochondrial DNA. 2011;22:130–142. doi: 10.3109/19401736.2011.624611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Queinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Worheide G, Manuel M. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 2009;19:706–712. doi: 10.1016/j.cub.2009.02.052. [DOI] [PubMed] [Google Scholar]
  21. Ren J, Shen X, Jiang F, Liu B. The mitochondrial genomes of two scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): the most highly rearranged gene order in the family Pectinidae. J Mol Evol. 2010;70:57–68. doi: 10.1007/s00239-009-9308-4. [DOI] [PubMed] [Google Scholar]
  22. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33:W686–689. doi: 10.1093/nar/gki366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schneider A. Import of RNA into mitochondria. Trends Cell Biol. 1994;4:282–286. doi: 10.1016/0962-8924(94)90218-6. [DOI] [PubMed] [Google Scholar]
  24. Signorovitch AY, Buss LW, Dellaporta SL. Comparative genomics of large mitochondria in placozoans. PLoS Genet. 2007;3:e13. doi: 10.1371/journal.pgen.0030013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Smietanka B, Burzynski A, Wenne R. Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: rapidly evolving atp8. J Mol Evol. 2010;71:385–400. doi: 10.1007/s00239-010-9393-4. [DOI] [PubMed] [Google Scholar]
  26. Vanfleteren JR, Vierstraete AR. Insertional RNA editing in metazoan mitochondria: the cytochrome b gene in the nematode Teratocephalus lirellus. RNA. 1999;5:622–624. doi: 10.1017/s135583829999009x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Zhang P, Zhou H, Chen YQ, Liu YF, Qu LH. Mitogenomic perspectives on the origin and phylogeny of living amphibians. Syst Biol. 2005a;54:391–400. doi: 10.1080/10635150590945278. [DOI] [PubMed] [Google Scholar]
  28. Zhang P, Zhou H, Liang D, Liu YF, Chen YQ, Qu LH. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene. 2005b;346:133–143. doi: 10.1016/j.gene.2004.10.012. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

01