Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships.

BACKGROUND: Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS: We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS: Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.

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.

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.

Complete mitochondrial genome of Mustela sibirica (Carnivora: Mustelidae), a protected and endangered species in China.

We sequenced the complete mitochondrial genome (mitogenome) of Mustela sibirica in China by the shotgun genome skimming methods. The mitogenome of M. sibirica is 16,558bp in length with the base composition of 32.9% A, 27.3% T, 26.0% C, and 13.9% G, and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one non-coding control region. The 13 PCGs use ATG as initiation codons except ND3, ND5 and ND2 which initiate with codons ATA and ATT, respectively. Four (COX3, ND1, ND2 and ND4) of the 13 PCGs terminate with a single T- -, and the remainder with a TAA termination codon except ND3 and CYT B using TA- and AGA as termination codon. The phylogenetic tree based on 13 protein-coding genes indicated that M. sibirica is sister to the clade grouped with three species M. nigripes, M. eversmannii, and M. putorius, and Mustelinae species formed a monophyletic group, which is close to the Lutrinae clade within Mustelidae.

Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model.

To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China's temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1-M23) and 15 nuclear alleles (N1-N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima's D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.

Complete mitochondrial genome of Rhus gall aphid Meitanaphis microgallis (Hemiptera: Aphididae: Eriosomatinae).

We sequenced the complete mitochondrial genome of the Chinese Rhus gall aphid Meitanaphis microgallis (Hemiptera: Aphididae: Eriosomatinae: Fordini) by the genome skimming method on an Illunima platform. The assembled mitogenome is 16,191 bp in length with a very high A + T content of 84.3%. This genome consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. All the protein-coding genes have a typical ATN initiation codon and TAA termination codon except COX1 and ND4 with a single T as stop codon. The tRNAs ranged in size from 59 to 77 bp and formed a clover-leaf secondary structure except tRNA-Ser (AGN). We constructed the phylogenetic relationship of Fordini aphids including all the Rhus gall aphids, and the ML tree showed that M. microgallis grouped with M. elongallis as its sister group.

Complete mitochondrial genome of Capreolus pygargus (Cervidae: Capreolinae), a protected and threatened species in China.

We sequenced the complete mitochondrial genome (mitogenome) of Siberian Roe Deer, Capreolus pygargus, in China by the shotgun genome-skimming methods. The mitogenome of C. pygargus is totally 16,353 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The sequence has a higher A + T content of 63.4% than G + C 36.6% and with a base composition of 33.4% A, 23.2% C, 13.4% G, and 30.0% T. All of the 13 PCGs initiate a typical ATN codon except Nd4L with GTG. Six PCGs terminate with a TAA codon, while Cyt b, Atp8, and Nd1 terminate with AGA, TAG, and TA-, respectively. Whereas, Cox3, Nd2, Nd3, and Nd4 terminate with a single T-. The phylogenetic trees of the subfamily Capreolinae with 13 PCGs indicated that Capreolus species were well-supported as a monophyletic group, which is sister to the clade of Hydropotes with well-support.

Complete mitochondrial genome of Prionailurus bengalensis (Carnivora: Felidae), a protected species in China.

The complete mitochondrial genome (mitogenome) of the leopard cat Prionailurus bengalensis in China was sequenced using the shotgun genome-skimming method. The mitogenome of P. bengalensis is totally 17,006 bp in length with a higher A + T content of 60.4% than that of G + C and consists of 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region. All the PCGs initiate with a typical ATN codon and terminate with a TAA codon except for the four PCGs (COX1, ND2, ND3, and ND4) terminating with a single T-and one gene CYT B with AGA as stop codon. Most of the tRNA genes have a clover-leaf secondary structure except for tRNAS (AGN), which loses a dihydrouridine (DHU) arm. The ML phylogenetic tree showed that P. viverrinus nested in the group of P. bengalensis individuals, which is close to the clade clustered by the two genera Otocolobus and Felis.