The complete mitochondrial genome of Euplatypus parallelus (Coleoptera: Curculionidae)

Abstract

Beetles in the weevil subfamily Platypodinae are among the dominant groups of insects in wet tropical forests, which together with bark and ambrosia beetles in the subfamily Scolytinae. Easily recognised by the circle-shaped entrance holes in fallen logs and a very elongated body shape, they have earned the common name, “pinhole borers”. All except two Platypodinae species are ambrosia beetles that cultivate fungi in wood tunnels as the sole food for their larvae. Platypodinae is a peculiar weevil subfamily of species that cultivate fungi in tunnels excavated in dead wood. The Platypodinae is likely the oldest known lineage of fungus-cultivating insects, with an origin of the ambrosial habit more than 80 Ma. Here, we sequenced and characterized the complete mitochondrial genome of E. parallelus, which was collected from logs imported from SierraLeone. The complete circular mitochondrial genome (mitogenome) of Euplatypus parallelus is 16,095 bp in size, containing 37 typical genes and one non-coding AT-rich region. The AT content of the AT-rich region is 87.5%. All protein-coding genes (PCGs) start with standard ATN initiation codons except for nad1and end with complete termination codons TAA except for cox1genes using an incomplete stop codon T. tRNA genes are predicted with a characteristic cloverleaf secondary structure except for trnS1^(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop. The size of the large and small ribosomal RNA genes are 1386 and 741 bp, respectively.

Keywords:

• Euplatypus parallelus
• mitochondrial genome
• Coleoptera

Curculionidae is a largest family of Coleoptera with more than 50,000 species worldwide. To date, 1200 species have been recorded in China. Despite this large taxonomic diversity, information about the Curculionidae mitogenomes is still limited. Platypodinae is a peculiar weevil subfamily of the Curculionidae, which has the most prominent economic meaning (Kirkendall & Faccoli 2010). Molecular biological techniques are widely applied to insect systematics (Leavitt et al. 2013). The specimen of E. parallelus was collected from logs imported from SierraLeone (About 6 degrees xiking 12 degrees north latitude) in February 2013, was stored in animal laboratory in Shaanxi Normal University with an accession number is 130221, identified by researcher Xin-Guo Wang of Huangpu Exit-Entry Inspection and Quarantine Bureau Guangzhou (Figure 1).

Figure 1. The BI phylogenetic tree of E. parallelus based on 13 PCGs dataset. The BI phylogenetic tree of E. parallelus. A BI phylogenetic tree was reconstructed using 13 PCGs, GTR + I+G was selected as the best model, and with one Termitidae species as outgroups. Numbers on each node indicate the bootstrap value. Leaf names were presented as species names and Genbank accession number.

The complete mitogenome of E. parallelus is a closed circular molecule of 16,095 bp in length, with the typical gene content as other known Coleoptera mitogenomes: 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rrnL and rrnS), 13 PCGs, and 1 major non-coding AT-rich region (Table 1). Its gene order and orientation are identical to those of other beetles. In addition to the AT-rich region, 11 intergenic spacers (366 bp in total) and 15 overlapping regions (71 bp in total) are dispersed throughout the whole genome. The nucleotide composition of A, T, C, and G are 41.6%, 34.5%, 14.4%, and 9.5%, respectively. The overall nucleotide content is significantly biased toward AT (A + T content =76.1%). Analysis of base composition at each codon position of the concatenated 13 PCGs showed that the first codon position (81.0%) is higher in A + T content than the second (66.8%) and third (73.0%) positions. All PCGs are initiated by a typical ATN codon (five with ATT, three with ATG, and four with ATA), except for four genes (nad1). Twelve PCGs have a complete stop codon, while the cox1 gene end with a single nucleotide T. Analysis of 22 tRNA of E. parallelus shows the characteristic cloverleaf secondary structure, except for trnS1^(AGN) which lacked the dihydrouridine (DHU) arm and replaced by a single loop. The rrnL and rrnS of the E. parallelus are 1386 bp and 741 bp, respectively. Furthermore, the two rRNAs are also significantly biased towards AT nucleotides (77.60% for rrnL and 77.20% for rrnS). trnI locates in AT-rich region and divided into two sections.

Table 1. Annotation of mitochondrial genome of E. parallelus.

Gene	Direction	Position	Size (bp)	Intergentic Length^a	Anti codon	Start codon	Stop codon
trnQ	R	1–69	69		UUG
trnM	F	69–137	69	1	CAU
nad2	F	138–1145	1008	0		ATT	TAA
trnW	F	1145–1199	55	1	UCA
trnC	R	1213–1274	62	−13	GCA
trnY	R	1279–1343	65	−4	GUA
cox1	F	1336–2875	1540	8		ATT	T
trnL2^(UUR)	F	2876–2938	63	0	UAA
cox2	F	2939–3619	681	0		ATT	TAA
trnK	F	3622–3692	71	−2	CUU
trnD	F	3692–3754	63	1	GUC
atp8	F	3755–3910	156	0		ATT	TAA
atp6	F	3907–4578	672	4		ATA	TAA
cox3	F	4578–5360	783	1		ATG	TAA
trnG	F	5365–5427	63	−4	UCC
nad3	F	5428–5778	351	0		ATT	TAA
trnA	F	5777–5837	61	2	UGC
trnR	F	5838–5899	62	0	UCG
trnN	F	5897–5962	66	3	GUU
trnS1^(AGN)	F	5963–6029	67	0	UCU
trnE	F	6029–6092	64	1	UUC
trnF	R	6091–6154	64	2	GAA
nad5	R	6154–7872	1719	1		ATA	TAA
trnH	R	7873–7935	63	0	GUG
nad4	R	7935–9260	1326	1		ATA	TAA
nad4L	R	9257–9550	294	4		ATA	TAA
trnT	F	9557–9619	63	−6	UGU
trnP	R	9620–9683	64	0	UGG
nad6	F	9686–10,192	507	−2		ATT	TAA
cob	F	10,196–11,332	1137	−3		ATG	TAA
trnS2^(UCN)	F	11,342–11,406	65	−9	UGA
nad1	R	11,433–12,389	957	−26		TTG	TAA
trnL1^(CUN)	R	12,391–12,455	65	−1	UAG
rrnL	R	12,416–13,801	1386	40
trnV	R	14,098–14,161	64	−296	UAC
rrnS	R	14,161–14,901	741	1
AT-rich region		14,902–16,095	1194	0
trnI	F	15,558–15,621	64	64	AAU

^a The positive number indicates interval base pairs between genes, while the negative number indicates the overlaping base pairs between genes.

Nucleotide sequence accession number

The complete genome sequence of E. parallelus has been assigned GenBank accession number KX711704.

Disclosure statement

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

Additional information

Funding

This work was supported in part by Qinling insect resources investigation (Grant No. 4010665), Rapid Sequencing of the ambrosia beetles Mitochondrial Genome Using Illumina Technology and phylogenetic analysis (Grant No. cx16118) and Resource utilization of Apis cerana cerana and ecological protection in Qingling Daba Mountain Area (Grant No. cx16027).