The mitochondrial genome of the brown citrus aphid Aphis (Toxoptera) citricidus: Insights into the repeat regions in aphids and phylogenetic implications

Complete Mitochondrial Genome and Phylogenetic Position of Nurudea zhengii Ren (Insecta, Hemiptera, Aphididae)

Nurudea zhengii Ren was identified by aphid morphological characteristics as well as the gall shape and host plant species, and placed in the tribe Fordini (Hemiptera, Aphididae, Eriosomatinae). Here, its whole genome was firstly sequenced by a genome-skimming method and its mitochondrial genome (mitogenome) was assembled to examine its genetic variation and phylogenetic position. The complete mitogenome of Nurudea zhengii is 15,392 bp in length, and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs and one D-loop region. The gene order follows the mitogenomes of the other Rhus gall aphids, and similarly has an AT bias with the content of 83.9%. The majority strand is A-skewed and C-skewed, and shows opposite skewness for G-skewed in the minority strands. The ratios of nonsynonymous to synonymous substitution rates of protein-coding genes are lower than one except for ATP8, which indicated that ATP8 was undergoing positive selection. Phylogenetic analysis among the Rhus gall aphids based on 13 protein-coding genes and two rRNA genes showed that N. zhengii was sister to N. shiraii, and then clustered with N. yanoniella as a group with high support value. The two species, N. shiraii and N. yanoniella, share the same host plant Rhus chinensis, while the host of N. zhengii is R. hypoleuca. However, the phylogenetic relationship indicated that the taxa sharing the same host plant were not absolutely clustered as the closest taxa at least at species level.

Complete mitochondrial genome of Stethoconus japonicus (Hemiptera: Miridae): Insights into the evolutionary traits within the family Miridae

The mitochondrial (mt) genome sequence of insects possesses numerous evolutionary traits. To better understand the evolution of mt genomes within the family Miridae, the complete mt genome of the predatory Japanese plant bug Stethoconus japonicus Schumacher was sequenced before undertaking a comparative analysis of all reported plant bug mt genomes. The mt genome of S. japonicus is a closed-circular and double-stranded DNA molecule of 16,274 bp (GenBank: MK341530), which consists of 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and a putative control region (CR). Consistent with other plant bugs, the mt genome of S. japonicus is strongly AT-biased (73.49 %) with A-skewed (0.202) and C-skewed (-0.248). All 13 PCGs initiate translation using ATN codons and TAA served as complete stop codons for eight PCGs, which as incomplete stop codon "T-" for cox1, nad1, nad5-6 and "TA-" for cox2. Regarding other features, all 22 tRNAs could be folded into typical cloverleaf secondary structures. The control region is 1,717 bp and contains a long tandem repeat sequence of a 165 bp unit repeated six times. Similar sequence with variable number of tandemly repeated units from intra-genus CRs is a distinct characteristic of plant bug mt genomes. Phylogenetic relationships of 15 bugs were eventually analyzed based on Maximum likelihood (ML) and Bayesian inference (BI) methods using 17 mt genome sequences. In the phylogenetic trees, species from a same genus or subfamily are clustered into a branch with high supporting values.and the result suggest that Deraeocorinae is more closely related to Mirinae than Bryocorinae. Finally, this study revealed that mutation of tRNA anticodon is a useful phylogenetic marker that could be of significance for studies of evolutionary patterns.

Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.

Insights into the Evolution of Aphid Mitogenome Features from New Data and Comparative Analysis

The complete mitochondrial genomes and their rearrangement patterns can provide useful information for inferring evolutionary history of organisms. Aphids are one of the insect groups with some unique mitogenome features. In this study, to examine whether some features in aphid mitogenomes are independent species-specific evolutionary events or clade-specific events at certain taxonomic levels, we sequenced three new aphid mitogenomes (Hormaphidinae: Ceratovacuna keduensis, Pseudoregma panicola; Lachninae: Nippolachnus piri) and compared them with all known aphid mitogenomes. The three mitogenomes are 16,059–17,033 bp in length, with a set of 37 typical mitochondrial genes, a non-coding control region and a tandem repeat region. The gene orders of them are all highly rearranged. Within the subfamily Hormaphidinae, the presence of repeat region and mitogenome rearrangement in Cerataphidini species but not in the other two tribes indicate that these may be Cerataphidini-specific features. The same gene rearrangement pattern in the two Lachninae species, N. piri (Tuberolachnini) and Stomaphis sinisalicis (Stomaphidini), supports that this feature should be at least derived from the common ancestor of two tribes. Overall, our data and analyses provide new insights into the evolutionary patterns of gene rearrangement and repeat region in aphid mitogenomes, and further corroborate the potential role of gene rearrangement in elucidating the evolutionary history of different insect lineages.

Comparative mitochondrial genomes of the Rhus gall aphid Kaburagia rhusicola subspecies with variable gall shapes

Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae) stimulate the formation of galls on their primary host plants (sumacs: Rhus spp., Anacardiaceae). The shapes of galls are often used as an extended phenotype to identify the aphid species and subspecies. We collected four Rhus galls with conspicuously different shapes formed by Kaburagia rhusicola aphids, whose sequences of the complete mitochondrial genomes (mitogenomes) were obtained by high-throughput sequencing. Each mitogenome was assembled into a circular molecule containing 13 protein-coding genes, two rRNAs, 22 tRNAs and one control region. All the protein-coding genes had a typical ATN initiation codon and TAA termination codon except for cox1 and nad4, which had a single T as stop codon. All the tRNAs could be folded as a typical clover-leaf secondary structure, except for trnS1 lacking a dihydrouridine (DHU) arm. The relative synonymous codon usage and ratio of nonsynonymous to synonymous substitution rates showed that the four K. rhusicola samples were highly similar to the subspecies K. r. ovogallis. The phylogenetic analyses grouped these samples with K. r. ovogallis in a clade sister to K. r. rhusicola. All these molecular analyses demonstrated that our current samples represented one subspecies of Kaburagia rhusicola, i.e., K. r. ovogallis, and the gall shape was variable even at the subspecies level in Kaburagia gall aphids.

Characterization of the complete mitochondrial genome of a barklouse, Lepinotus sp. (Psocodea: Trogiomorpha: Trogiidae)

Barklice in the genus Lepinotus (Psocoptera: Trogiidae) are small, soft-bodied stored-product pests that are difficult to control. We sequenced and annotated the mitochondrial (mt) genome of Lepinotus sp. The mt genome of Lepinotus sp. is 16,299 bp in size with 74.4% A + T content. The gene order was highly conserved in some of the Trogimorpha barklice. Two types of tandem repeat units were identified in CR of Lepinotus sp. The phylogenetic analysis showed that Trogiidae species was the sister group to Lepidopsocidae barklice, and the suborder Troctomorpha was polyphyletic.

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.

The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region

Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.

The first complete mitochondrial genome of Adelges tsugae Annand (Hemiptera: Adelgidae)

Hemlock wooly adelgid (HWA), Adelgests ugae Annand (Hemiptera: Adelgidae), is a species native to Asia but later ravages Endangered hemlock forests (Tsuga spp.) in eastern North America. In this study, we obtained the first complete mitochondrial genome of HWA (16,509 bp in length) using meta-genomic sequencing method. The HWA mitogenome has a general gene annotation as other aphids, comprising 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Our phylogenetic result showed Aphidoidea is sister to Coccoidea and the newly sequenced mitogenome is put on the correct position, sister to Adelgeslaricis.

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.