The brown spider Loxosceles similis (Araneae: Sicariidae): complete mitochondrial genome sequence

Abstract

The Brazilian brown spider Loxosceles similis (Moenkhaus, 1898) is, like others from the same genus, an arachnid that can cause serious accidents, which is called loxoscelism. Here, we present the complete mitochondrial genome sequence (mtDNA) of L. similis. The whole DNA molecule is 14,683 bp long, contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a non-coding Control Region (D-loop) of 851 bp. The majority of the protein-coding genes (PCGs) were found on the heavy strain, with the exception of the genes ND1, ND4, ND4L, and ND5. Six different start codons were found. Seven of the PCGs contained a TAG termination codon, and one (ND4) contained an incomplete ‘T–‘ stop codon.

Keywords:

• Spider
• complete mtDNA
• Loxosceles similis
• brown spider
• Sicariidae

Materials, results and discussion

Loxosceles (Heineken & Lowe, 1832) is the genus of spiders of medical importance that causes most of the accidents in Brazil (SINAN 2016). This genus is widely distributed in temperate and tropical areas (Gertsch 1967). The envenoming caused by spider bites of the genus Loxosceles is called loxoscelism and can lead to dermonecrotic lesions and renal problems (Silvestre et al. 2005; Dantas et al. 2016).

Genomic DNA was extracted from the body (except the abdomen) of one female individual collected in the municipality of Felício dos Santos (18° 03’51.9” S/43° 12’55.1” W), state of Minas Gerais, Brazil (voucher 20191Ls, collection LBMM-ICB-UFMG). Following maceration on dry ice, the DNA was purified using magnetic beads (AMPure XP, GE Healthcare). A genomic library was constructed and sequenced using a paired-end 600 cycle strategy on a MiSeq platform (Illumina^®). The generated reads were filtered, trimmed, and assembled de novo using Geneious R11.1.5 (Kearse et al. 2012). The complete mtDNA (GenBank accession number MK425700) was found to be circular and 14,683 bp-long. The full mtDNA sequence contained 27.22% of GC. The individual bases were found in the following proportions: 30.56% of A, 42.22% of T, 18.13% of G, and 9.09% of C. Annotation was performed using MITOS Web Server (Bernt et al. 2013) for identification of the genes, start and stop codons. Genes were also manually verified using the GenBank, ExPASy Translate tool and also based on the work of Masta and Boore (2004), Kim et al. (2016), and Pan et al. (2016).

The mitochondrial genome presented two rRNA, 13 protein-coding genes (PCGs), 22 tRNA, and one control region (D-loop). We found four genes (ND1, ND3, ND4, and ND4L) starting with an ATA initiation codon, three genes (ND2, ATP6, and COX3) starting with ATG start codon, and three genes (CytB, ND5, and ND6) starting with an ATT initiation codon. The remaining genes COX1, COX2, and ATP8 started with TTA, GTG, and ATC, respectively. Seven PCGs (ND2, ATP8, ATP6, ND5, ND6, CytB, and ND1) had a TAG stop codon, five genes (COX1, COX2, COX3, ND3, and ND4L) contained a TAA stop codon, and one gene (ND4) contained a ‘T–’ stop codon, which is completed to TAA by posttranscriptional polyadenylation. Four of the 13 PCGs (ND5, ND4, ND4L, and ND1) were located in the light strand. Three overlapping regions were found between the genes ATP8 and ATP6, ND5 and ND4, and ND4 and ND4L. The D-loop non-coding region contained 73.09% of AT and was 851 bp-long. Ten of 22 tRNAs (trnA, trnC, trnY, trnL2, trnF, trnH, trnP, trnL1, trnV, and trnQ) were found on the light strand. The two rRNAs were also found on the light strand. A phylogenetic tree was built using 19 sequences of mitochondrial genomes (without the D-loop non-coding region) of arachnids and the L. similis mitogenome using the software MEGA version 7.0.26 (Figure 1).

Figure 1. Consensus phylogenetic tree inferred from 20 mitochondrial genomes of arachnids without the non-coding D-loop region. The tree comprises three suborders, nine superfamilies and 11 families of Arachnida class. Tityus serrulatus was used as outgroup. The consensus tree was constructed using the Kimura 2-parameter method, with 1000 bootstrap. The numbers indicate the sustenance of each clade. Loxosceles similis is inserted into Araneomorphae and, among the species analyzed, is the phylogenetically closest species of Pholcus phalangioides, both Haplogynae, as suggested by Ramírez (2000) and Michalik and Ramírez (2014). All sequences were obtained from the GenBank database, and the accession numbers are presented in the figure.

Acknowledgements

We thank Mr. Heitor Bispo and Mr. Hiran Caldeira Victória for their essential contribution to this work. We also thank the support of Phoneutria Biotecnologia & Serviços (PHT).

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Additional information

Funding

This work was funded by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (Edital Ciências Forenses no. 25/2014, Process 23038.006839/2014-33), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) APQ-00826-17, and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) 307550/2015-0.