ABSTRACT
We announce the nearly complete mitochondrial genome sequences of two hexactinellid sponges, Bathydorus laniger and Docosaccus maculatus. A contiguous region of over 15,000 bp was sequenced from each genome. An uncommon structural element was identified as a series of repetitive elements with sequences matching cob in the genome of D. maculatus.
GENOME ANNOUNCEMENT
We sequenced the nearly complete mitochondrial genomes of two abyssal sponges (phylum Porifera), bringing the total coverage to 13 hexactinellid genomes. Tissue samples from the holotypes of Bathydorus laniger Kahn et al. 2013 and Docosaccus maculatus Kahn et al. 2013 were collected in 2007 from Station M, 200 km west of Point Conception, CA (4,100 m depth [1]). Tissue samples were frozen in liquid nitrogen and stored at −80°C. DNA was extracted under liquid nitrogen according to DNeasy animal and blood tissue extraction kit protocols (Qiagen, USA). Mitochondrial DNA (mtDNA) was sequenced using primer walking with standard PCR, long PCR (2), and restriction digestion and cloning. Sequences were assembled using Geneious version 5.3 (3). Coding regions were identified using BLAST searches (GenBank), followed by a comparison of gene translations in Geneious. tRNA sequences were predicted using tRNAscan-SE (4).
We sequenced 15,704 bp for Bathydorus laniger, 14,709 bp of which (93.7%) represents coding regions; the total A+T content was 71.3%. This included 29 genes, with 12 protein-coding genes (three units of cytochrome oxidase [cox1, cox2, and cox3], six subunits of NADH dehydrogenase [nad1, nad2, nad3, nad4, nad4L, and nad5], cytochrome b [cob], and two subunits of ATP synthase [atp6 and atp9]), small (rns) and large (rnl) subunit rRNAs, and 15 tRNAs. The largest noncoding space was 262 bp long, with no notable elements.
The coverage of the mitochondrial genome of Docosaccus maculatus was similar, with a single contiguous sequence of 17,143 bp, of which 15,212 bp (88.7%) represents coding regions; the A+T content was 70.9%. There were 32 genes, with the same 13 protein-coding genes as B. laniger plus NADH dehydrogenase subunit 6 (nad6), rns, and rnl, and 17 tRNAs.
In both species, most genes used ATG as a start codon, but the start codon for atp9 was ATA. The stop codons were either TAA or TAG. In D. maculatus, a +1 frameshift occurred in nad2 (amino acid position 63). The insertion was preceded by the UGG codon for tryptophan, which was present only there and once in cox1 of B. laniger; all other tryptophan residues were encoded by the more common UGA codon. Interestingly, the UGG codon has been associated with a +1 frameshift in coding regions of other glass sponges (5–7).
Noncoding mtDNA for D. maculatus was concentrated in a 1,439-bp region between nad1 and cob. It contained two stuttering repeats of trnY and the 5ʹ end of a partial cob sequence upstream of a functional cob gene. The region also included two nonfunctional copies of trnY (gua) and a third functional gene (predicted using tRNAscan-SE [4]) which differed by only a few base pairs from the other two. Repetitive regions have been found in demosponges as palindromic repeats (8–10) but have not been observed in hexactinellid species, and stuttering repeats of protein-coding genes have not been observed in any other sponge genomes; the feature is so far unique to D. maculatus.
Accession number(s).
Sequences have been deposited in DDBJ/ENA/GenBank under the accession numbers KJ634155 (Bathydorus laniger) and KJ634156 (Docosaccus maculatus).
ACKNOWLEDGMENTS
K. L. Smith, H. A. Ruhl, J. Ellena, M. Vardaro, the crew of the research vehicle (R/V) Western Flyer, and pilots of the remotely operated vehicles (ROVs) Tiburon and Doc Ricketts were responsible for the collection of sponge specimens. We thank N. B. Webster, G. Cailliet, K. L. Smith, and H. Hawk for reviewing the manuscript and providing constructive feedback.
Funding came from student support from the Marine Technology Society, the Dr. James Nybakken Scholarship administered by the Friends of MLML, and the David and Lucille Packard Foundation.
The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Kahn AS, Geller JB. 2018. Partial mitochondrial genome sequences of two abyssal sponges (Porifera: Hexactinellida), Bathydorus laniger and Docosaccus maculatus. Genome Announc 6:e00234-18. https://doi.org/10.1128/genomeA.00234-18.
REFERENCES
- 1.Smith KL Jr, Druffel ERM. 1998. Long time-series monitoring of an abyssal site in the NE Pacific: an introduction. Deep Sea Res II 45:573–586. doi: 10.1016/S0967-0645(97)00094-5. [DOI] [Google Scholar]
- 2.Burger G, Lavrov DV, Forget L, Lang BF. 2007. Sequencing complete mitochondrial and plastid genomes. Nat Protoc 2:603–614. doi: 10.1038/nprot.2007.59. [DOI] [PubMed] [Google Scholar]
- 3.Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Rosengarten RD, Sperling EA, Moreno MA, Leys SP, Dellaporta SL. 2008. The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: evidence for programmed translational frameshifting. BMC Genomics 9:33. doi: 10.1186/1471-2164-9-33. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Haen KM, Lang BF, Pomponi SA, Lavrov DV. 2007. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? Mol Biol Evol 24:1518–1527. doi: 10.1093/molbev/msm070. [DOI] [PubMed] [Google Scholar]
- 7.Haen KM, Pett W, Lavrov DV. 2013. Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation. Gene 535:336–344. doi: 10.1016/j.gene.2013.10.041. [DOI] [PubMed] [Google Scholar]
- 8.Wang X, Lavrov DV. 2007. Mitochondrial genome of the homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals. Mol Biol Evol 24:363–373. doi: 10.1093/molbev/msl167. [DOI] [PubMed] [Google Scholar]
- 9.Lukić-Bilela L, Brandt D, Pojskić N, Wiens M, Gamulin V, Müller WEG. 2008. Mitochondrial genome of Suberites domuncula: palindromes and inverted repeats are abundant in non-coding regions. Gene 412:1–11. doi: 10.1016/j.gene.2008.01.001. [DOI] [PubMed] [Google Scholar]
- 10.Lavrov DV. 2010. Rapid proliferation of repetitive palindromic elements in mtDNA of the endemic Baikalian sponge Lubomirskia baicalensis. Mol Biol Evol 27:757–760. doi: 10.1093/molbev/msp317. [DOI] [PubMed] [Google Scholar]