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Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma . Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.

Seed dormancy is a complex adaptive trait of plants that are influenced by several physiological and environmental factors. The endangered plant Cinnamomum migao is also known to exhibit seed dormancy and low germination, which may influence its regeneration; however, these characteristics remain unexplored. To our knowledge, this study is the first to examine the type of dormancy and improve the germination percentage of C. migao seeds. We evaluated the structure and characteristics of the embryo and endocarp of C. migao seeds as well as the effects of endogenous inhibitors. Furthermore, we assessed the effects of light, stratification, alternating temperature, and gibberellic acid 3 (GA 3 ) on the dormancy release of these seeds. The embryo was well developed the endocarp was water-permeable, and no obvious mechanical hindrance to germination was observed. However, the endocarp and embryo contained phenols and other germination inhibitors. The seed extracts of C. migao delayed the germination of cabbage and ryegrass seeds, which indicates the presence of endogenous inhibitors. These findings suggest that C. migao seeds exhibit physiological dormancy. Light and an alternating temperature (15/20°C) did not influence germination. However, GA 3 pretreatment, alternating temperatures, and warm stratification relieved dormancy. GA 3 pretreatment combined with the 15°C stratification treatment was most effective in rapidly releasing the C. migao seed dormancy. Our findings may facilitate the storage and conservation of this endangered plant, which is currently underrepresented in ex situ collections.

Background Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus , Caloglyphus berlesei , Dermatophagoides farinae , D. pteronyssinus , Histiostoma blomquisti and Psoroptes cuniculi . Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus ; loss of 2–3 tRNA genes was reported in Tyrophagus longior , T. putrescentiae and Sarcoptes scabiei . Nevertheless, convincing evidence for mt gene loss is lacking in these mites. Results We sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini , respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus , two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae , and the two mt tRNA genes that were reported as lost in Sa. scabiei . All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems. Conclusions Our results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.

Background Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters—some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. Results Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. Conclusions This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

Local adaptation is particularly likely in invertebrate pests that typically have short generation times and large population sizes, but there are few studies on pest species investigating local adaptation and separating this process from contemporaneous and historical gene flow. Here, we use a population genomic approach to investigate evolutionary processes in the two most dominant spider mites in China, Tetranychus truncatus Ehara and Tetranychus pueraricola Ehara et Gotoh, which have wide distributions, short generation times, and large population sizes. We generated genome resequencing of 246 spider mites mostly from China, as well as Japan and Canada at a combined total depth of 3,133×. Based on demographic reconstruction, we found that both mite species likely originated from refugia in southwestern China and then spread to other regions, with the dominant T. truncatus spreading ~3,000 years later than T. pueraricola. Estimated changes in population sizes of the pests matched known periods of glaciation and reinforce the recent expansion of the dominant spider mites. T. truncatus showed a greater extent of local adaptation with more genes (76 vs. 17) associated with precipitation, including candidates involved in regulation of homeostasis of water and ions, signal transduction, and motor skills. In both species, many genes (135 in T. truncatus and 95 in T. pueraricola) also showed signatures of selection related to elevation, including G‐protein‐coupled receptors, cytochrome P450s, and ABC‐transporters. Our results point to historical expansion processes and climatic adaptation in these pests which could have contributed to their growing importance, particularly in the case of T. truncatus.

Eriophyid mites (Eriophyidae) are strictly phytophagous and are concentrated in Europe, Eastern Asia, Southeast Asia, Western and Eastern North America, Southern India, and New Zealand. South and southwest China are hot spots for eriophyid mite species diversity and endemism. In this study, we describe two new species, Scolotosus ehretussp. nov. on Ehretia acuminata (Boraginaceae) and Neotegonotus ulmchangussp. nov. on Ulmus changii (Ulmaceae), from south and southwest China (the Oriental Region), and one new eriophyid mite, Leipothrix ventricosissp. nov. on Hosta ventricosa (Asparagaceae), from northeast China (the Palearctic Region). All three new eriophyid mite species are distributed in the temperate region of China. We further provided mitochondrial gene (cox1, 12S rRNA) and nuclear gene (18S rRNA, 28S rRNA) sequences for three new species.

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. F. occidentalis, which is endemic to North America, was initially detected in Kunming in southwestern China in 2000 and since then it has rapidly invaded several other localities in China where it has greatly damaged greenhouse vegetables and ornamental crops. Controlling this invasive pest in China requires an understanding of its genetic makeup and migration patterns. Using the mitochondrial COI gene and 10 microsatellites, eight of which were newly isolated and are highly polymorphic, we investigated the genetic structure and the routes of range expansion of 14 F. occidentalis populations in China. Both the mitochondrial and microsatellite data revealed that the genetic diversity of F. occidentalis of the Chinese populations is lower than that in its native range. Two previously reported cryptic species (or ecotypes) were found in the study. The divergence in the mitochondrial COI of two Chinese cryptic species (or ecotypes) was about 3.3% but they cannot be distinguished by nuclear markers. Hybridization might produce such substantial mitochondrial-nuclear discordance. Furthermore, we found low genetic differentiation (global F(ST) = 0.043, P<0.001) among all the populations and strong evidence for gene flow, especially from the three southwestern populations (Baoshan, Dali and Kunming) to the other Chinese populations. The directional gene flow was further supported by the higher genetic diversity of these three southwestern populations. Thus, quarantine and management of F. occidentalis should focus on preventing it from spreading from the putative source populations to other parts of China.

The center-periphery hypothesis (CPH) states that the genetic diversity, genetic flow, and population abundance of a species are highest at the center of the species' geographic distribution. However, most CPH studies have focused on the geographic distance and have ignored ecological and historical effects. Studies using niche models to define the center and periphery of a distribution and the interactions among geographical, ecological, and historical gradients have rarely been done in the framework of the CPH, especially in biogeographical studies of animal species. Here, we examined the CPH for a widely distributed arthropod, Tetranychus truncatus (Acari: Tetranychidae), in eastern China using three measurements: geographic distance to the center of the distribution (geography), ecological suitability based on current climate data (ecology), and historical climate data from the last glacial maximum (history). We found that the relative abundances of different populations were more strongly related to ecology than to geography and history. Genetic diversity within populations and genetic differentiation among populations based on mitochondrial marker were only significantly related to history. However, the genetic diversity and population differentiation based on microsatellites were significantly related to all three CPH measurements. Overall, population abundance and genetic pattern cannot be explained very well by geography alone. Our results show that ecological gradients explain the variation in population abundance better than geographic gradients and historical factors, and that current and historical factors strongly influence the spatial patterns of genetic variation. This study highlights the importance of examining more than just geography when assessing the CPH.

Eriophyoidea represents a highly diverse superfamily of herbivorous mites in the Acariformes, including over 5,000 named species that are distributed worldwide. However, the lack of chromosome-level genome prevents our understanding of the evolution in this group. Here, we report the first chromosome-level genome assembly of Setoptus koraiensis using Illumina, PacBio, and Hi-C sequencing technologies. The assembled genome has a size of 47 Mb with an N50 of 24.53 Mb, anchored into two chromosomes. The chromosome-level genome assembly had a BUSCO completeness of 89%. We identified 5,954 protein-coding genes, with 4,770 genes that could be functionally annotated. This genome provides resources to further understand the genetic and evolution of eriophyoid mites.

The Eriophyoidea, notable for specific morphological characters (four-legged mites) and gall-formation in host plants (gall mites), is one of the most species-rich superfamilies of Acari. Monophyly of the superfamily Eriophyoidea is accepted by all acarologists; however, monophyly of most genera has not been evaluated in a molecular phylogenetic network. Furthermore, most eriophyoid mites, especially species in the genus Diptilomiopus, are morphologically similar, challenging their identification. Here we test the phylogeny and cryptic diversity of Diptilomiopus species using fragments of two mitochondrial (COI and 12S) and two nuclear (18S and 28S) genes. Our results revealed the monophyly of Diptilomiopus. Sequence distance, barcode gap, and species delimitation analyses of the COI gene allowed us to resolve cryptic diversity of Diptilomiopus species. Additionally, we supposed that characteristics of genu fused with femur on both legs and seta ft′ absent on leg II evolved only once within Diptilomiopus, which are potential morphological synapomorphies. In contrast, characteristics of both setae ft′ and ft″ divided into a short branch and a long branch were supposed evolving multiple times independently. Our findings contribute to the understanding of phylogeny and morphological evolution of Diptilomiopus species and provide a DNA-based approach for species delimitation of Diptilomiopus mites.