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. 2022 Jun 14;7(6):1032–1034. doi: 10.1080/23802359.2022.2081098

The complete mitogenome of Plator insolens (Araneae: Trochanteriidae) with phylogenetic implication

Yuhui Ding a, Hongru Xu a, Huiqin Ma b, Junxia Zhang a,b,✉
PMCID: PMC9225705  PMID: 35756453

Abstract

Plator insolens Simon, 1880 belongs to the family Trochanteriidae and is distributed in China. Herein, we report the complete mitochondrial genome of P. insolens reconstructed from Illumina sequencing data, which is the first published mitochondrial genome for the family. The mitogenome is 14,519 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. The phylogenetic analysis indicates that P. insolens is clustered within the RTA clade of the infraorder Araneomorphae. This study provides useful genetic information for future studies on the taxonomy, phylogeny and evolution of trochanteriid species.

Keywords: Mitochondrial genome, NGS technique, phylogenetic analysis, RTA clade

Plator insolens Simon, 1880, belonging to the family Trochanteriidae, is mainly distributed in Hebei and Henan provinces and occasionally found in Liaoning province of China (Zhu and Zhang 2011). The Trochanteriidae Karsch, 1879 is a relatively small spider family with six genera and 50 species currently known worldwide (World Spider Catalog 2022). Members of this group are commonly known as flattened spiders due to their dorsoventrally flattened bodies which may be an adaptation to life in cracks and under tree barks (Zhu and Zhang 2011; Azevedo et al. 2021). The mitochondrial genomes have provided valuable insights on the evolution of various animal groups (e.g. Nardi et al. 2003; Fujita et al. 2007). However, no complete mitogenome has yet been published for the family Trochanteriidae. Here we performed high-throughput sequencing on a specimen of P. insolens from China to determine its mitogenome structure and its phylogenetic relationship with other 19 spider species.

Specimens of Plator insolens were collected from Xiong County, Baoding City, Hebei Province, China (38°58′09″N, 116°02′46″E). The spider sampling was permitted by the Institute of Life Science and Green Development, Hebei University (The name and number of the project are the Open Foundation of Hebei Key Laboratory of Wetland Ecology and Conservation, No. hklk201910). The voucher specimen (YHD022) is deposited at the Museum of Hebei University (Yuhui Ding, email: dingyuhui@stumail.hbu.edu.cn). The genomic DNA was extracted with the DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany). The sequencing library was produced using the NEXTFLEX Rapid DNA-Seq Kit 2.0 (Bioo Scientific, Austin, USA) and following the manufacturer’s protocol. The prepared library was sequenced on the Illumina Novaseq 6000 platform with 150 bp paired-end reads at Novogene (Tianjin, China). Approximately 4.97 Gbp of raw data were obtained, which were proceeded with quality control to remove reads of low quality (with ≥10% unidentified nucleotides, or with > 50% bases having Phred quality < 5, or with > 10 nt aligned to the adapter, or the read 1 and read 2 of two paired-end reads that were completely identical). The remaining cleaned data were used to assemble the complete mitochondrial genome using Meng et al. (2019). Genome annotation was first performed with the annotation module in Mitoz, and then further polished in the MITOS web server (Bernt et al. 2013). The mitochondrial DNA sequence of P. insolens with the annotated genes was deposited in GenBank (accession number: OM397542).

The complete mitogenome of P. insolens is circular with 14,519 bp in length. It has 37 mitochondrial genes (13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNA genes) that are typically present in metazoan mitogenomes (Boore 1999). Among the 37 genes, 23 are encoded on the major strand (J-strand) while the others are encoded on the minor strand (N-strand). The gene composition is identical to those found in other spider mitogenomes (Pan et al. 2014; Zhu and Zhang 2017). However, the order of some tRNAs (L: tRNA-Leu, E: tRNA-Glu, A: tRNA-Ala) is apparently different from that of other spider species (Figure 1). The mitogenome of P. insolens shows a high nucleotide bias with 71.9% of A + T and 28.1% of G + C (31.3% A; 40.6% T; 19.7% G; and 8.4% C). Among the 13 protein-coding genes (PCGs), most of them start with ATA (COX1, COX3, ND3, ND5, ND4L, ND6, CYTB) or ATT (ND2, ATP6, ND1), and two starts with TTG (ATP8, ND4), and one start with GTG (COX2). Eight PCGs are terminated with TAA (ND2, COX1, ATP6, COX3, ND3, ND4, ND6, ND1). One PCG ends with TAG (COX2) and one ends with an incomplete stop codon (ND6).

Figure 1.

Figure 1.

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Bayesian phylogenetic analysis of 20 species based on the combined 13 protein-coding genes (numbers along the branch are posterior probabilities). Accession numbers of the mitochondrial sequences used in the phylogenetic analysis are listed in brackets after species. The rectangle, rhombus and ellipse in gene order represent coding genes, tRNA and rRNA respectively.

We constructed the phylogenetic relationships of 20 spider species based on the mitochondrial genome data to test the placement of P. insolens in the spider phylogeny. Bayesian inference (BI) based on the nucleotide sequences of the 13 PCGs was conducted using MrBayes 3.2.6 (Ronquist et al. 2012) under the GTR + I + G + F model. The 13 PCGs were extracted and concatenated using PhyloSuite v1.2.1 (Zhang et al. 2020). The phylogenetic tree (Figure 1) shows that P. insolens is clustered within the RTA clade of the infraorder Araneomorphae, which is consistent with the result of a recent UCE phylogenomic study (Kulkarni et al. 2021).

Acknowledgments

We thank Yaozhuo Wang for her assistance with analysis of the data.

Funding Statement

This work was funded by the following grants to Junxia Zhang: the Open Foundation of Hebei Key Laboratory of Wetland Ecology and Conservation (Grant No. hklk201910), the Advanced Talents Incubation Program of the Hebei University (Grant No. 521000981324), and the National Natural Science Foundation of China (Grant No. 32070422).

Author contributions

Junxia Zhang and Huiqin Ma planned the research and contributed to the fieldwork; Yuhui Ding and Hongru Xu performed the experiments and data analyses; Yuhui Ding and Junxia Zhang took the lead in preparing the manuscript, and all authors contributed to the discussion and final manuscript.

Disclosure statement

The authors report no conflicts of interest. The authors themselves are responsible for the content and writing of the paper.

Data availability statement

The mitogenome sequence data of Plator insolens has been deposited in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. OM397542. The associated Bio-Project, SRA, and Bio-Sample numbers are PRJNA817674, SRR18355032, and SAMN26804931 respectively.

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Associated Data

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

Data Availability Statement

The mitogenome sequence data of Plator insolens has been deposited in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. OM397542. The associated Bio-Project, SRA, and Bio-Sample numbers are PRJNA817674, SRR18355032, and SAMN26804931 respectively.

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