Abstract
The complete mitochondrial genome of Homidia socia was assembled from the Illumina sequencing data. The circularized genome spans 14,793 bp with a high A + T content of 75.1% and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The most common start and stop codon for 13 PCGs are ATT and TAA, respectively. A phylogeny of 16 collembolan species clustered this species within Entomobryidae.
Keywords: Mitogenome, Entomobryoidea, gene order, phylogeny
The genus Homidia is among the most dominant entomobryid springtails in eastern Asia (Bellinger et al. 1996‒2019) but its systematic position within Entomobryidae remains unclear. It is possibly related to one of the Entomobrya lineages based on three molecular markers (Ding et al. 2019). To date, a few short mitochondrial and ribosomal sequences have been reported for Homidia (NCBI, accessed 2019 Jun 15). To explore its evolution in Collembola, we report the complete mitochondrial genome of Homidia socia Denis, representing the first mitogenome of the genus.
In this study, we collected specimens of H. socia from Taizhou, Zhejiang Province, China (28.657°N, 121.505°E, NCBI BioSample accession SAMN11651000). The specimen (specimen Accession number 4595) and its DNA were deposited in the Nanjing Agricultural University, Nanjing, China. Genomic DNA was extracted from a single individual using a QIAamp DNA Micro Kit (Qiagen, GmbH, Germany) and sequenced by NovaSeq 6000, generating 9.78 Gbp of raw reads (NCBI SRA accession SRR9056946). The mitogenome was assembled with NOVOPlasty v2.7.2 (Dierckxsens et al. 2017), annotated with MitoZ v2.4-alpha (Meng et al. 2019), and deposited in GenBank (accession MN480464).
The circularized mitogenome of H. socia is 14,793 bp in length, and contains 13 protein-coding genes (PCGs), 22 transfer (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The gene order is identical to putative ancestral pancrustacean pattern. The overall nucleotide composition is 38.6% A, 14.7% C, 10.2% G, 36.5% T, indicating an obvious A + T bias (75.1%). Both AT-skew (0.028) and GC-skew (0.181) are positive. For the 13 PCGs, three start codons are found: ATG (ND2, ATP6, ND4, CYTB), ATA (ATP8, ND6), and ATT (other seven PCGs); three stop codons are present: TAG (COX2, ND3), T (COX1, COX2, ND4L) and TAA (other eight PCGs). The length of tRNAs varies from 61 to 72 bp and all have the typical cloverleaf structure except for trnS1, which lacks a dihydrouridine arm.
Each PCG was aligned with MAFFT v7.394 (Katoh and Standley 2013) and trimmed using trimAl v1.4.1 (Capella-Gutiérrez et al. 2009) with the heuristic method ‘automated1’. A phylogenetic tree was constructed based on 13 PCGs using IQ-TREE v1.6.10 (Nguyen et al. 2015) with the site heterogeneous model PMSF (Wang et al. 2018). Monophyly of three orders (Symphypleona, Poduromorpha, Entomobryomorpha) is absolutely supported with Homidia socia clustered within Entomobryidae (Figure 1).
Figure 1.
Maximum-likelihood phylogenetic tree inferred from 13 PCGs using PMSF model. SH-aLRT and UFBoot support values are given on nodes.
Disclosure statement
No potential conflict of interest was reported by the authors.
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