Nearly complete mitochondrial genome of Siobla xizangensis Xiao, Huang & Zhou, 1988 (Hymenoptera: Tenthredinidae) and phylogenetic analysis

Abstract

In this study we review the phylogenetic grouping of the sawfly genus Siobla within the superfamily Tenthredinoidea. Using Next Generation Sequencing (NGS), we describe the complete mitochondrial genome of Siobla xizangensis Xiao, Huang & Zhou, 1988. The assembled mitochondrial genome of S. xizangensis was found to be 15015 bp, with three tRNA genes rearranged compared to the ancestral organization. The overall nucleotide composition was 42.6% for A, 11.4% for C, 7.7% for G and 38.3% for T. The phylogenetic tree based on heterogeneity models of 36 Symphytan and two Apocritan recovered the monophyly of Tenthredinidae, and S. xizangensis was identified as the sister group of Tenthredo.

Systematic studies of the genus Siobla (Hymenoptera, Tenthredinoidea, Tenthredinidae, Sioblinae) have recently been performed (Niu and Wei 2010). Within the genus, a range of morphological characteristics were reported according to the species groups (Niu et al. 2012; Niu and Wei 2013). However, significant inconsistencies with the position of Siobla within the superfamily Tenthredinoidea have been reported. Here, we describe the nearly complete mitochondrial genome of S. xizangensis Xiao et al. 1988 to advance our understanding of the phylogenetic status of Siobla amongst the Tenthredinoidea.

Samples of S. xizangensis were collected in Mêdog 52 K, Tibet Autonomous Region (29.74°N 95.68°E) in 2019. The specimens (CSCS-Hym-MC0150) used to obtain the samples were taken are available at the Asia Sawfly Museum, Nanchang (ASMN) repository. Whole genomic DNA was extracted from the specimen’s thorax muscle using the DNeasyR Blood & Tissue Kits (Qiagen, Valencia, CA). Genomic DNA was sequenced by the high-throughput Illumina Hiseq 4000 platform, yielding a total of 42756724 raw reads (SRR10207561). DNA sequences were assembled using MitoZ (Meng et al. 2019), and Geneious Prime 2019.2.1 (https://www.geneious.com) using S. sturmii (unpublished) as reference, the mean coverage is 21135. Annotations were generated in MITOS web server (Bernt et al. 2013) and revised in Geneious Prime when necessary.

Upon initial attempts, the nearly complete mitochondrial genome of S. xizangensis was found to be 15015 bp in length and accessible on GenBank (accession number MN562486). Furthermore, the analysis yielded a genome containing 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA (rRNA) genes. The ancestral pattern of A + T rich region-trnI(+)-trnQ(-)-trnM(+) clusters were rearranged to trnQ(-)-trnM(-)- A + T rich region -trnI(+). There are five gene overlaps among atp8-atp6 (7 bp), atp6-cox3 (1 bp), trnE and trnF (2 bp), nad4-nad4L (4 bp) and nad6-cob (1 bp). There are 14 gene intervals among nad2-trnW (14 bp), trnC-trnY (1 bp), cox2-trnK (3 bp), cox3-trnG (6 bp), nad3-trnA (4 bp), trnA-trnR (4 bp), trnR-trnN (16 bp), trnS1-trnE (3 bp), trnF-nad5 (2 bp), trnH-nad4 (6 bp), nad4L-trnT (2 bp), trnP-nad6 (2 bp), trnS2-nad1 (7 bp), trnQ-trnM (4 bp). The rrnS and rrnL genes were 809 bp and 1334 bp in length, respectively, and located between trnL1 and trnQ, separated by trnV. The base composition was 34.8% (A), 10.3% (C), 9.9% (G) and 44.9% (T), with a high A + T content (79.8%) of PCGs. The length of the PCGs accounted for 74.9% of the mitogenome. Only cox1 start with GTG, the remainder PCGs start with typical ATN codon. cox1 and cob are terminated with incomplete stop codon T, and the remaining PCGs with the stop codon TAA.

The eleven unsaturated amino acids (atp8 and nad4L were excluded) of 36 Symphytan and two Apocritan were aligned in TranslatorX (Abascal et al. 2010) subjected to Bayesian analysis with PhyloBayes (Lartillot et al. 2009) under the MtArt-CAT model conducted on the CIPRES (Miller et al. 2010) webserver (Figure 1). All related files have been uploaded to figshare (https://figshare.com/account/home#/projects/70835). S. xizangensis was identified as the sister group of Tenthredo.Furthermore, phylogeny inference under the heterogeneous model confirmed that Athalia was a basal lineage amongst the Tenthredinoidea (He et al. 2019), and that Pamphiliidae and Megalodontesidae are recovered as monophyletic Pamphilioidea (Niu et al. 2019).

Figure 1.

Phylobayes tree based on the combined data of eleven unsaturated amino acids. Numbers above each node are posterior probabilities. The accession number for each species is indicated after the Latin name.