The complete mitochondrial genome of a parthenogenetic ant Monomorium triviale (Hymenoptera: Formicidae)

Abstract Monomorium is one of the most species-rich yet taxonomically problematic ant genus. An East Asian species, M. triviale Wheeler, W.M., 1906, is reproduced by obligate thelytokous parthenogenesis and performs strict reproductive division of labor. We sequenced the M. triviale mitogenome using next-generation sequencing methods. The circular mitogenome of M. triviale was 16,290 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single non-coding region of 568 bp. The base composition was AT-biased (82%). Gene order rearrangements were detected and likely to be unique to the genus Monomorium. We announce the M. triviale mitogenome as additional genomic resources for elucidating phylogenetic and taxonomic problems of Monomorium and comparative genomics of parthenogenetic ant species.

In the hyperdiverse ant subfamily Myrmicinae, Monomorium Mayr, 1855 is one of the most species-rich genera with over 300 described species including several successful tramp species such as the flower ant M. floricola and M. salomonis, and the pharaoh ant M. pharaonis (Pontieri and Linksvayer 2019). However, recent studies (Ward 2015;Sparks 2019) suggest polyphyly of this genus, and genomic resources are therefore essential for resolving such a taxonomic issue.
An East Asian species, M. triviale Wheeler, W.M., 1906 is particularly of our interest as it reproduces by thelytokous parthenogenesis where virgin queens produce both workers and next-generation queens (Gotoh et al. 2012;Idogawa et al. 2021). To date, only partial mitochondrial DNA sequences have been reported, with all of which being identical among populations in Japan (Idogawa et al. 2021). Hence, a complete mitochondrial genome of this species can provide additional information for further analysis. Here, we present the first complete mitogenome for M. triviale.
A colony of M. triviale headed by a single queen was collected in Takaragaike Park,Kyoto,Japan (35.060087 N,135.788488 E) on 9 September 2017. The queen and her parthenogenetic offspring produced later in the laboratory (larvae and pupae, approximately 100 individuals) were fixed in 99.5% EtOH. We extracted genomic DNA from the pooled individuals with DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany). We sequenced the pooled DNA on the HiSeq X sequencer (Illumina, San Diego, CA) at Macrogen Japan Corp.
The complete mitogenome of M. triviale was 16,920 bp in length, which is comparable to those of other ant species. The nucleotide composition was AT-biased (82%). The mitogenome contained 13 PCGs, two rRNAs, and 22 tRNAs, which are typical for most metazoan animals. All PCGs used ATG or ATT as the start codon and TAA or TAG as the stop codon. The tRNAs, ranging in size from 59 to 74 bp, were similar to those of other ants (54-90 bp). The control region presumably corresponded to the single largest non-coding AT-rich region (569 bp, A þ T 94%). Gene order of M. triviale was identical to that of a congener M. pharaonis (NC_051486.1). Notably, the gene order of the two Monomorium species had two gene rearrangements: an inversion between trnP and ND1 (Myrmicinae, ND6-CYTB-trnS; Monomorium, trnS-CYTB-ND6; underlines indicate inverted genes) and translocations between ND3 and trnF (Myrmicinae common, trnA-trnR-trnN-trnS-trnE; Monomorium, trnR-trnE-trnA-trnN-trnS). This feature was different from the common gene order of the subfamily Myrmicinae and likely unique to Monomorium ants (Babbucci et al. 2014;Park 2020). This may help identify the genus Monomorium sensu stricto, in addition to nucleotide substitutions.
We inferred the phylogenetic relationships of 25 ant species using the concatenated nucleotide sequences of all 13 PCGs, with the honeybee Apis mellifera as an outgroup. Sequence alignment was constructed using ClustalW (Thompson et al. 2003) implemented in MEGA-X (Kumar et al. 2018). The GTR þ I þ G model was determined as a best-fit model by ModelTest-NG v0.1.6 (Darriba et al. 2020). Both a maximum-likelihood tree made by RAxML-NG v1.0.0 (Kozlov et al. 2019) and Bayesian inference tree made by MrBayes v3.2.7 (Ronquist et al. 2012) consistently support the current phylogenetic placement of Monomorium in the subfamily Myrmicinae (Figure 1).
In conclusion, the newly sequenced complete mitochondrial genome of M. triviale provides additional resources for further phylogenetic characterization of the taxonomically problematic genus Monomorium and comparative genomics of parthenogenetic ant species.