Comparative mitochondrial genome analysis of Daphnis nerii and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships

Abstract

In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Daphnis nerii (Lepidoptera: Sphingidae) is described. The mitogenome (15,247 bp) of D.nerii encodes13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced lepidopterans. The 12 PCGs initiated by ATN codons except for cytochrome c oxidase subunit 1 (cox1) gene that is seemingly initiated by the CGA codon as documented in other insect mitogenomes. Four of the 13 PCGs have the incomplete termination codon T, while the remainder terminated with the canonical stop codon. This mitogenome has six major intergenic spacers, with the exception of A+T-rich region, spanning at least 10 bp. The A+T-rich region is 351 bp long, and contains some conserved regions, including ‘ATAGA’ motif followed by a 17 bp poly-T stretch, a microsatellite-like element (AT)9 and also a poly-A element. Phylogenetic analyses based on 13 PCGs using maximum likelihood (ML) and Bayesian inference (BI) revealed that D. nerii resides in the Sphingidae family.

Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera: Sphingidae)

“…The GC skews of the seven Sphingidae species are all negative and the AT skews are positive except for M. sexta (-0.005) and A. convolvuli (-0.001) ( Sun et al 2017 ; Xin et al 2017 ; Dai et al 2016).…”

“… convolvuli (81.49%), and A. rubiginosa (81.5%) ( Sun et al 2017 ; Xin et al 2017 ; Dai et al 2016). The AT skew and GC skew of T. japonica J-strand are 0.023 and -0.245 respectively (Table 2 ).…”

“…Mitochondrial DNA sequences have been widely used to study the molecular evolution of insects due to protein-coding genes ( PCGs ) sequence conservatism, maternal inheritance, and rapid evolution ( Cameron 2014 ). In Sphingidae , however, only the complete mitochondrial DNA sequences of Notonagemia analis ( KU934302 ) ( Kim et al 2016 ), Sphinx morio ( KC470083 ) ( Kim et al 2013 ), Manduca sexta ( EU286785 ) ( Cameron and Whiting 2008 ), Ampelophaga rubiginosa ( KT153024 ) ( Xin et al 2017 ), Agrius convolvuli ( https://doi.org/10.1139/gen-2016-0058 ) ( Dai et al 2017 ), and Daphnis nerii ( https://doi.org/10.1371/journal.pone.0178773.s001 ) ( Sun et al 2017 ) have been reported up to now. Among these six species, N. analis , S. morio , A.…”

Comparative mitochondrial genome analysis of Dendrolimus houi (Lepidoptera: Lasiocampidae) and phylogenetic relationship among Lasiocampidae species

“…With the development of next generation sequencing technology (NGS) [33][34][35], the use of high-throughput sequencing technology has provided great convenience for the rapid acquisition of mitogenome [35][36][37], and the sequencing cost has also been significantly reduced in recent years, which provides an alternative choice for the sequencing of small genomes such as animal mitochondria [37]. Mitogenomes are more comprehensive and accurate in species identification and phylogeny, avoiding artificial biases caused by blindness of a single gene [38][39][40][41][42][43], and even the differences among species can be determined based on genes structure and arrangement, which has higher reliability [31,43]. Methodologically, using the 13 PCGs in the sequencing genome was superior in obtaining reliable results compared with clustering analysis by using individual genes [44][45][46][47][48][49][50], while both two clustering trees by using both methods were consistent, and the https://doi.org/10.1371/journal.pone.0232527.g004…”

The complete mitochondrial genome of the Papilio paris (Lepidoptera: Papilionidae)

“…The A þ T-rich region is 533 bp long and contains some conserved regions, including 'ATAGA' motif followed by a 11 bp poly-T stretch and a microsatellite-like element (AT) 8 . The length of poly-T stretch varies from species to species (Dai et al 2015;Sun 2019), whereas ATAGA region is conserved in Lepidoptera species (Sun, Chen, et al 2017).…”