The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe

Abstract

The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species – D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.

The Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications

“…The GTG initiation codon seems to be characteristic for the ATP8 gene of the species of the Bactrocera subgenus [53][54][55][56][62][63][64]83,84]. Three of the PCGs possess an incomplete termination codon (Table 1); TA for COI, which is characteristic for all Bactrocera species analyzed so far and T for ND1 and ND5 similarly to the majority of tephritids [52][53][54][55][56][57][58][59][60][61][62][63][64][81][82][83][84][85][86][87][88]. Incomplete termination codons are common in animal mitochondrial DNA and are likely to be completed by post-transcriptional polyadenylation [89].…”

“…Partial mitochondrial sequences have been extensively used for exploring relationships among species of the Bactrocera genus; however, they had their limitations, for instance in the discrimination among closely related members of the B. dorsalis complex [9,10,12,14,15,25,27,[36][37][38][39][40][41]. On the other hand, complete mitochondrial genome sequences, which are accumulating rapidly in databases nowadays, have proven to be a valuable alternative approach for phylogeny reconstruction and molecular systematics in several insect groups [42][43][44][45][46][47][48][49][50], including Tephritidae [51][52][53][54][55][56][57][58][59][60][61][62][63][64]. Especially, when the discrimination of closely related species is attempted, the comparative analysis of complete mitogenomes can help to select the most informative mitochondrial markers/sequences for specific issues [53].…”

Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini)

“…We constructed an alignment of mitochondrial COI barcode sequences from genome sequencing projects of six dacine species: Bactrocera oleae (AY210702, Nardi et al, 2003), B. tryoni (HQ130030, Nardi et al, 2010), B. dorsalis (DQ845759, Yu et al, 2007), B. minax (HM776033, Zhang et al, 2014, Zeugodacus cucurbitae (JN635562, Wu et al, 2013), and Dacus longicornis (KX345846, Jiang et al, 2016). We also included three identified numt sequences from B. tryoni (JQ420918-JQ420920, Blacket et al, 2012).…”

The complete mitochondrial genome of the hymenopteran hunting robber fly Dasypogon diadema

“…If necessary, the annotations were corrected manually. Compared to other dipteran mitochondrial genomes (Jiang et al 2016;Qi et al 2017) the arrangement of the protein-coding genes in Dasypogon diadema is identical.…”