The complete mitochondrial genome of the smallest known free-living insect Scydosella musawasensis.

The mitochondrial genome of the smallest known free-living insect Scydosella musawasensis (Polilov, 2015) is published in this paper. The mitochondrial DNA (mtDNA) is 14 719 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes and 21 tRNA genes. The overall base composition of the genome in descending order was 40.59% - A, 13.85% - C, 36.82% - T and 8.73% - G, with a significant AT bias of 77.41%.

Scydosella musawasensis individuals were collected in Chicaque National Park, Colombia, 10 km west of Bogotá, 2200 m above sea level, on the fungus Steccherinum sp. (Meruliaceae). Specimens were deposited in the entomological collection of the Zoological Museum of Lomonosov Moscow State University (ZMMU I-P-00844-854). DNA was extracted using NucleoSpin Tissue XS kit (Macherey-Nagel, Germany). DNA-libraries were constructed using Ovation Ultralow Systems V2 kit (NuGEN, San Carlos, CA). Mitochondrial genome was sequenced used Illumina Hiseq 1500 (Illumina, USA) with 100 bp pared-end reads.

Totally 226 571 628 Illumina paired-end reads were generated. Reads were merged (up to 60%) using Pear software (Zhang et al. 2014). After PCR-duplicate trimming, we used MITObim software (Hahn et al. 2013) and mitogenome of the American carrion beetle Necrophila americana (Coleoptera: Silphidae) as reference sequence for reconstructing the mitochondrial genome of S. musawasensis.

Surprisingly, we did not find trnI gene in our assembly. SPAdes software was used for de novo assembly (Bankevich et al. 2012) as proof that trnI is absent in S. musawasensis mitogenome. Totally 249 988 contigs were assembled (N50 = 1314 bp), but contigs mapping on the MITObim assembly did not yield a trnI gene in mitogenome.

As a result, the mitogenome of S. musawasensis consists of 14 719 bp (GenBank accession number: KU302777), including 13 protein-coding genes (PCGs), 2 rRNA genes and 21 tRNA genes. Despite that arthropod mitochondrial DNA typically contain the 22 tRNAs (Boore 1999), our data showed that S. musawasensis have lost trnI gene.

Six of the 13 PCGs (COX1, NAD5, NAD4L, NAD6, COB, NAD1) used ATT as a start codon, and other three (NAD2, COX2, NAD4) used ATA, ATP6 started with ATG codon, ATP8 and NAD3 with ATC, and COX3 with CAC. Three genes (ATP8, COX2, NAD3) ended with a TGA stop codon, NAD1, NAD5 and NAD4L ended with ATT, NAD2 and NAD4 ended with AAA, COX1 gene ended with a TTA codon, ATP6 with TCT, COX3 with AGT, NAD6 with CGA, and COB with ATT. The rrnL and rrnS genes were located between trnL1(tag) and trnQ(ttg) genes, with 631 and 739 bp in length, respectively.

The phylogenetic analysis was performed for the Staphylinoidea superfamily and other Coleoptera species (Phacomorphus fratyi (KT780668.1); Sciodrepoides watsoni (KT780675.1); Tetartopeus terminatus (NC_028613.1); Sepedophilus bipunctatus (NC_028611.1); Scaphidium quadrimaculatum (NC_028609.1); Pselaphinae sp. 5 EF-2015 (KT780684.1); Pselaphinae sp. 4 EF-2015 (KT780682.1); Aleocharinae sp. 6 EF-2015 (KT780687.1); Aleocharinae sp. 5 EF-2015 (KT780685.1); Oxypoda acuminata (NC_028606.1); Rugilus geniculatus (NC_028608.1); Olophrum piceum (NC_028605.1); Myrmecocephalus concinnus (NC_028604.1); Liogluta microptera (NC_028602.1); Gabronthus thermarum (NC_028601.1); Euryusa optabilis (NC_028600.1); Dacrila fallax (NC_028599.1); Callicerus obscurus (NC_028598.1); Atrecus affinis (NC_028597.1); Thinonoma atra (KT780699.1); Necrophila americana (NC_018352.1); Euspilotus scissus (NC_018353.1); Margarinotus merdarius (NC_028603.1); Sphaeridium bipustulatum (NC_028612.1); Tropisternus sp. BYU-CO166 (NC_018349.1) and Tetraphalerus bruchi (NC_011328.1) (Figure 1). For phylogenetic analysis, 9 protein-coding genes (COX3, ATP6, COX2, COX1, NAD5, NAD4, NAD4L, NAD6, and COB) and 9 transfer RNAs were used as marker genes. The phylogenetic tree was constructed by neighbor-Joining method, using the MEGA5.0 (Tamura et al. 2011).

Figure. 1.

Neighbor-Joining tree for Scydosella musawasensis, Staphylinoidea superfamily and other Coleoptera species and primitive beetle Tetraphalerus bruchi as outgroup based on sequence of 9 protein-coding genes (COX3, ATP6, COX2, COX1, NAD5, NAD4, NAD4L, NAD6, and COB) and 9 transfer RNAs.