Comparison of complete mitochondrial DNA sequences between old and new world strains of the cowpea aphid, Aphis craccivora (Hemiptera: Aphididae)

The complete mitochondrial genome of Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) isolated from Leonurus japonicus in Korea

We have determined the mitochondrial genome of A. gossypii isolated from Leonurus japonicus in Korea. The circular mitogenome of A. gossypii is 16,044 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 797 bp. AT ratio is 83.8%. 88 SNPs and 4 INDELs (175 bp) were identified against mitogenome of A. gossypii isolated from cotton species. Especially, largest INDEL (170 bp) was in the control region. Phylogenetic trees show that four A. gossypii mitogenomes were clustered in one clade.

Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts

Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.

Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae)

The complete mitochondrial genomes of aphids Aphis fabae mordvilkoi, A. craccivora, Myzus persicae from Aphidinae as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae were sequenced and compared with the genomes of other aphid species. A. fabae mordvilkoi, Th. tenera and A. robiniae mitogenomes were sequenced and analyzed for the first time. The annotation of A. craccivora and M. persicae were corrected compared to what was previously published. According to our data there is no translocation of tRNA-Tyr gene in A. craccivora mitogenome and this aphid species has an ancestral type of mitochondrial gene order. A + T content in all 5 mitogenomes was higher than 80%. A + T content in the Th. tenera CR was 59.5% which is untypically low. CRs of all 5 studied mitogenomes had 2 conserved motifs at their ends and extended G + C rich region. A. craccivora, M. persicae and Th. tenera had large tandem repeats inside the CRs. Detailed molecular analysis of all 5 aphid mitochondrial genomes showed the importance of a deep understanding of the molecular organization of all the functional regions of the mitochondrial DNA, which helps to avoid mistakes during genome annotation.

Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha)

The complete mitochondrial genome of the soybean aphid (Aphis glycines Matsumura), a major agricultural pest in the world, is described for the first time, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, as well as a large repeat region between tRNA-Glu and tRNA-Phe, and an AT-rich control region. The 17,954 bp mtgenome is the largest reported from the family Aphididae, and its gene order follows the ancestral insect mtgenome except for the repeat region, which contains a 195 bp unit repeated 11.9 times, representing the highest reported repeats among the known aphid mtgenomes to date. A new molecular phylogeny of Aphidae is reconstructed based on all available aphid mtgenomes, and it is shown that the mtgenome data can robustly resolve relationships at the subfamily level, but do not have sufficient phylogenetic information to resolve deep relationships. A phylogeny-based comparative analysis of mtgenomes has been performed to investigate the evolution of the repeat region between tRNA-Glu and tRNA-Phe. So far, among aphids, 13 species are known to have this repeat region of variable lengths, and a phylogenetic analysis of the repeat region shows that a large proportion of the sequences are conserved across the phylogeny, suggesting that the repeat region evolved in the most recent common ancestor of Aphidinae and Eriosomatinae, and that it has gone through numerous episodes of lineage-specific losses and expansions. Combined together, this study provides novel insights into how the repeat regions have evolved within aphids.

The mitochondrial genome of Greenidea psidii van der Goot (Hemiptera: Aphididae: Greenideinae) and comparisons with other Aphididae aphids

The complete mitochondrial genome of Greenidea psidii was sequenced and compared with the genomes of other aphid species. The G. psidii mitogenome is 16,202 bp long with an A + T content of 85.4%, comprising 37 genes arranged in the same order as the inferred insect ancestral arrangement, a control region and a special repeat region between trnE and trnF. G. psidii is the first representative possessing such a repeat region from the subfamily Greenideinae. These repeat motifs found in Aphidinae, Eriosomatinae and Greenideinae are species-specific, differing in nucleotide composition, length and copy number across different species. All reported complete aphid mitogenomes are A- and C-skewed in the whole genomes and show opposite skewness for C and G between the majority and minority strands. The ratios of nonsynonymous to synonymous substitution rates indicated that the evolution of the aphid mitogenomes has been dominated by purifying selection. Based on whole mitogenome sequences, the phylogenetic relationships among all aphid species with complete mitogenomes were investigated. G. psidii was robustly clustered with Cervaphis quercus, confirming its affiliation with the subfamily Greenideinae.

The complete mitochondrial genome of Anoplocnemis curvipes F. (Coreinea, Coreidae, Heteroptera), a pest of fresh cowpea pods

The complete 16,345-bp mitochondrial genome of the agriculturally destructive pod sucking pest, the giant coreid bug, Anoplocnemis curvipes (Hemiptera: Coreidae), was assembled from paired-end Illumina HiSeq 2500 reads. The A. curvipes mitochondrial genome consists of 13 protein coding genes (PCGs), 22 tRNAs, 2 rRNAs and a control region in the order and orientation typical among insects. PCG initiation codons (ATG, ATC, ATT and ATA) with termination codon (TAA) are used with the exception of TAG stop codons by Cytb and ND3. All tRNA genes fold into predicted cloverleaf secondary structures having requisite triplets on the anticodon loop, apart from tRNA-Ser1 (AGN) whose dihydrouridine (DHU) arm forms a simple loop. The phylogenetic analysis of hemipteran mitogenomes clusters to the family level and supports the monophyly of the five superfamilies in Pentatomomorpha of Hemiptera. The Coreoidea and Pyrrhocoroidea are sister groups, while Coreidae and Alydidae are sister groups to Rhopalidae. These analyses provide insight to mitogenomics and evolutionary relationships among pentatomoid insects.