Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

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The morphology of the two marine hypotrichous ciliates Apokeronopsis bergeri and A. ovalis, isolated from the Yellow Sea, Korea, are described based on live and protargol-impregnated specimens. It is the first time that these species have been recorded in Korea. In addition, the small subunit ribosomal RNA gene was sequenced for comparison with the public database. The genus Apokeronopsis has recently been established in the family Pseudokeronopsidae, and the two congeners of the Korean population share the following characteristics: one row of one or more buccal cirri; usually two frontoterminal cirri; midventral complex composed of two distinctly separated rows; one left and one right marginal row; number of transverse cirri, more than eight; absence of caudal cirri; two types of cortical granules. Apokeronopsis bergeri differs from A. ovalis primarily in body shape (fusiform vs. oval form), size (usually 260×80 μm vs. 160×55 μm), type II cortical granules (oval vs. round shape; yellow-green vs. mostly colourless and only a few yellow-green in colour), and morphometric data (75-106 vs. 53-70 in adoral membranelles; 37-47 vs. 24-36 in frontal cirri; 9-15 vs. 1-2 in buccal cirri), as well as molecular data (2.87% of pairwise distance).

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We present the complete mitochondrial genome of the Antarctic barnacle Lepas australis (Cirripedia, Thoracica, Lepadidae). The genome sequence is 15,502 bp in size. Except for CO1, 12 protein-coding genes (PCGs) start with an ATN initiation codon (ATA, ATG, ATC and ATT). Twelve PCGs were terminated with TAA or TAG stop codon, whereas ND1 possessed an incomplete termination codon (T- -). We compared the mitogenome structure of L. australis to those of other cirripeds and a typical arthropod Homarus americanus. The PCGs in the L. australis mtgenome showed a typical gene arrangement, identical to the arthropod pattern in other cirriped genomes. However, at least 8 tRNA genes were translocated and 2 tRNA genes were inverted in the coding polarity. Unique differences in L. australis mtgenome included translocation of trnS2, trnD and trnI. These results are useful for understanding the phylogenetic relationships among cirripedians, and additional mtgenome information of barnacles including the polar species would allow exploration of the thoracican relationships and mtgenome modifications in the barnacle evolution.