De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

Development of Simple Sequence Repeat of Monochamus alternatus (Coleoptera: Cerambycidae) Based on Restriction Site-Associated DNA Sequencing

Monochamus alternatus, a pest posing a serious threat to coniferous species, such as Pinus massoniana, has had devastating effects on pine forests due to its association with Bursaphelenchus xylophilus. The creation of unique simple sequence repeat (SSR) primers for M. alternatus is crucial, as there has been little study of the species' phylogeography. The aim of this study was to identify and create polymorphic SSR primers by sequencing samples of M. alternatus obtained from three different sampling points using the restriction site-associated DNA sequencing (Red-seq) approach. Subsequently, supplementary samples were integrated, and genetic typing was performed utilizing the identified polymorphic primers. Through comprehensive analysis, a total of 95,612 SSR loci were identified. Among these, mononucleotide repeats (51.43%), dinucleotide repeats (28.79%), and trinucleotide repeats (16.74%) predominated among the SSR motif types. Ultimately, 18 pairs of SSR primers were screened out, demonstrating stable amplification and high polymorphism. Genetic typing revealed that the mean number of alleles (Na) for these primer pairs ranged from 3 to 8, observed heterozygosity (Ho) ranged from 0.133 to 0.733, polymorphic information content (PIC) ranged from 0.294 and 0.783, and Shannon's index (I) ranged from 0.590 to 1.802. This study effectively produced 16 pairs of SSR primers that can be applied to different populations of M. alternatus. As a result, important tools for furthering studies on the phylogeography of pine wood nematodes, creating genetic maps, gene mapping, and carrying out in-depth investigations into gene function have been made available.

De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm

BACKGROUND

The cabbage webworm, Hellula undalis (Fabricius) (Lepidoptera: Pyralidae), is a significant pest of brassicas and other cruciferous plants in warm regions worldwide. Transcriptome analysis is valuable for investigation of molecular mechanisms underlying the insect development and reproduction. De novo assembly is particularly useful for acquiring complete transcriptome information of insect species when there is no reference genome available. In case of Hellula undalis, only 17 nucleotide records are currently available throughout NCBI nucleotide database. Genes associated with metabolic processes, general development, reproduction, defense and functional genomics were not previously predicted in the Hellula undalis at the genomic level.

METHODS & RESULTS

To address this issue, we constructed Hellula undalis transcriptome using Illumina NovaSeq6000 technology. Approximately 48 million 150 bp paired-end reads were obtained from sequencing. A total of 30,451 contigs were generated by de novo assembly of sample and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 71 % of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 123 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we compared the ortholog gene family of the Hullula undalis, transcriptome to Spodoptera frugiperda, spodotera litura and spodoptera littoralis and found that 391 orthologous gene families are specific to Hullula undalis. A total of 1,913 potential SSRs was discovered in Hullula undalis contigs.

CONCLUSIONS

This study is the first transcriptome data for Hullula undalis. Additionally, it serves as a valuable resource for identifying target genes and developing effective and environmentally friendly strategies for pest control.

Functional characterization of two DH44R genes associated with starvation and desiccation in Rhopalosiphum padi (Hemiptera: Aphididae)

CRF-like diuretic hormone receptor (CRF/DHR), also known as DH44R in insects, are G-protein coupled receptors (GPCRs) that play a role in regulating osmotic balance in various insect species. These receptors have the potential to be targeted for the development of insecticides. However, our understanding of the role of DHR genes in aphids, including Rhopalosiphum padi, a major wheat pest, is currently limited. In this study, we isolated and characterized two R. padi DHRs (RpDHR1 and RpDHR2). The expression levels of RpDHR1 increased after starvation and were restored after re-feeding. The expression levels of RpDHR1 gene decreased significantly 24 h after injection of dsRNA targeting the gene. Knockdown of RpDHR1 increased aphid mortality under starvation conditions (24, 36, 48 and 60 h). Under starvation and desiccation condition, the aphid mortality decreased after knockdown of RpDHR1. This is the first study to report the role of DHR genes in the starvation and desiccation response of aphids. The results suggest that RpDHR1 is involved in the resistance of R. padi to starvation and dehydration, making it a potential target for insecticide development. Novel insecticides could be created by utilizing DHR agonists to disrupt the physiological processes of insect pests.

A relaxin receptor gene RpGPCR41 is involved in the resistance of Rhopalosiphum padi to pyrethroids

Rhopalosiphum padi is a global pest that poses a significant threat to wheat crops and has developed resistance to various insecticides. G protein-coupled receptors (GPCRs), known for their crucial role in signaling and biological processes across insect species, have recently gained attention as a potential target for insecticides. GPCR has the potential to contribute to insect resistance through the regulation of P450 gene expression. However, GPCRs in R. padi remained unexplored until this study. We identified a total of 102 GPCRs in R. padi, including 81 receptors from family A, 10 receptors from family B, 8 receptors from family C, and 3 receptors from family D. Among these GPCR genes, 16 were up-regulated in both lambda-cyhalothrin and bifenthrin-resistant strains of R. padi (LC-R and BIF-R). A relaxin receptor gene, RpGPCR41, showed the highest up-regulated expression in both the resistant strains, with a significant increase of 14.3-fold and 22.7-fold compared to the susceptible strain (SS). RNA interference (RNAi) experiments targeting the relaxin receptor significantly increase the mortality of R. padi when exposed to the LC50 concentration of lambda-cyhalothrin and bifenthrin. The expression levels of five P450 genes (RpCYP6CY8, RpCYP6DC1, RpCYP380B1, RpCYP4CH2, and RpCYP4C1) were significantly down-regulated following knockdown of RpGPCR41 in LC-R and BIF-R strains. Our results highlight the involvement of GPCR gene overexpression in the resistance of R. padi to pyrethroids, providing valuable insights into the mechanisms underlying aphid resistance and a potential target for aphid control.

RpUGT344J7 is involved in the reproduction switch of Rhopalosiphum padi with holocyclic life cycle

Many aphid species exhibit both cyclical parthenogenesis (CP) and the obligate parthenogenesis (OP) life history, which are genetically determined. In CP aphid lineages, the parthenogenetic individuals can switch from asexual to sexual reproduction quickly in response to environmental factors such as changes in photoperiod and temperature. However, the OP aphid lineages do not undergo sexual reproduction under any conditions. So far, mechanisms underlying the reproduction switch in CP aphids have not been fully elucidated. Rhopalosiphum padi, a serious worldwide insect pest of wheat, has both CP and OP lineages. Uridine diphosphate-glycosyltransferases (UGTs) are enzymes that participate in the metabolic detoxification of xenobiotics. Here, we identified 43 RpUGT genes from R. padi genome and transcriptome sequences, and found that: (1) the UGT content of the CP lineage was significantly higher than that in the OP lineage at the key time points when CP lineage mainly produce virginoparae, gynoparae, and males under inducing condition, while there were no significant difference under normal conditions; (2) RpUGT344J7 gene was highly expressed during the time points when CP lineages produce gynopara and males; (3) the critical time points for CP lineages to produce virginoparaee, gynoparae, and males were affected when the CP lineages were injected with dsRpUGT344J7; (4) the knockdown of RpUGT344J7 caused a significant reduction in the total number of virginoparae, gynoparae, and males in the offspring under inducing condition. The findings contribute to our understanding of the molecular mechanisms underlying the quick shift from asexual to sexual reproduction in aphid species.

UGT2B13 and UGT2C1 are involved in lambda-cyhalothrin resistance in Rhopalosiphum padi

Uridine diphosphate-glucuronosyltransferases (UGTs) are major multifunctional detoxification phase II enzymes involved in the metabolic detoxification of xenobiotics. However, their roles in insecticides resistance are still unclear. In this study, we identified two UGTs genes (UGT2B13 and UGT2C1) in Rhopalosiphum padi, a serious insect pest of wheat worldwide. Bioassays results showed that the resistance ratio of R. padi resistance strain (LC-R) to lambda-cyhalothrin (LC) was 2963.8 fold. The roles of UGT2B13 and UGT2C1 in lambda-cyhalothrin resistance were evaluated. Results indicated that the UGTs contents were significantly increased in the LC resistant strain of R. padi. UGT2B13 and UGT2C1 were significantly overexpressed in the LC-R strain. Transcription levels of UGT2B13 and UGT2C1 were relatively higher in the gut of LC-R strain. RNA interference (RNAi) of UGT2B13 or UGT2C1 significantly decreased the UGTs contents of the LC-R aphids and increased mortality of R. padi exposure to the LC50 concentration of LC. This study provides a new view that UGTs are involved in LC resistance of R. padi. The findings will promote further work to detailed the functions of UGTs in the metabolism resistance of insects to insecticides.

Development of EST-SSRs based on the transcriptome of Castanopsis carlesii and cross-species transferability in other Castanopsis species

Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C. carlesii leaves. A total of 149,380,224 clean reads were obtained, and 63,012 nonredundant unigenes with a mean length of 1,034 bp were assembled and annotated based on sequence similarity searches in the Nr, Nt, KO, SwissProt, PFAM, KOG, and GO databases. The results showed that only 5,559 (8.82%) unigenes were annotated in all seven databases, but 46,338 (73.53%) could be annotated in at least one database. A total of 31,459 potential EST-SSRs were identified in 18,690 unigenes, with an average frequency of one SSR approximately 2 kb. Among the 100 EST-SSR primer pairs designed, 49 primer pairs successfully produced the expected product by amplification, with a success rate of 49%, but only 20 primer pairs showed abundant polymorphisms. Polymorphisms were verified using 25 samples from C. carlesii in Qimen, Anhui. A total of 119 alleles were detected, with a mean number of alleles (Na) of 5.95 per locus and a mean polymorphism information content (PIC) of 0.6125. All the 20 newly developed EST-SSR markers were verified in other Castanopsis species (C. sclerophylla, C. lamontii, C. fargesii, C. eyrei and C. jucunda). Sixteen primer pairs showed successful amplification in all five Castanopsis species (80%), and the transferability ratios ranged from 90% to 100%. These developed EST-SSR markers can be applied to population genetic and germplasm evaluations of C. carlesii and related species.

De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer

Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.

Chemosensory proteins are associated with thiamethoxam tolerance in bird cherry-oat aphid Rhopalosiphum padi

Rhopalosiphum padi (L.) is an important cosmopolitan pest of cereal crops. Thiamethoxam is widely used for control R. padi in some regions. Chemosensory proteins (CSPs) are a class of transporter proteins in arthropods which play a key role in various physiological processes including response to insecticide exposure. However, the role of R. padi CSPs (RpCSPs) in insecticide binding and susceptibility has not been well clarified. In this study, we found that the expression levels of RpCSP1, RpCSP4, RpCSP5, RpCSP7, RpCSP10 were dramatically upregulated after exposure to thiamethoxam. Suppression of RpCSP4 and RpCSP5 transcription by RNA interference significantly enhanced the susceptibility of R. padi to thiamethoxam. Molecular docking and fluorescence competitive binding showed that RpCSP4 and RpCSP5 had high binding affinity with thiamethoxam. The present results prove that RpCSP4 and RpCSP5 are related to insecticide resistance through high binding affinity to reduce the toxicity of insecticide.

Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction

BACKGROUND

Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning.

RESULTS

The transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus.

CONCLUSIONS

This study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning.

Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers

The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.

The phylogenetic and evolutionary analyses of detoxification gene families in Aphidinae species

Detoxification enzymes play significant roles in the interactions between insects and host plants, wherein detoxification-related genes make great contributions. As herbivorous pests, aphids reproduce rapidly due to parthenogenesis. They are good biological materials for studying the mechanisms that allow insect adaptation to host plants. Insect detoxification gene families are associated with insect adaptation to host plants. The Aphidinae is the largest subfamily in the Aphididae with at least 2483 species in 256 genera in 2 tribes: the Macrosiphini (with 3/4 of the species) and the Aphidini. Most aphid pests on crops and ornamental plants are Aphidinae. Members of the Aphidinae occur in nearly every region of the world. The body shape and colour vary significantly. To research the role that detoxification gene families played in the process of aphid adaptation to host evolution, we analyzed the phylogeny and evolution of these detoxification gene families in Aphidinae. In general, the P450/GST/CCE gene families contract, whereas the ABC/UGT families are conserved in Aphidinae species compared to these families in other herbivorous insects. Genus-specific expansions of P450 CYP4, and GST Delta have occurred in the genus Acyrthosiphon. In addition, the evolutionary rates of five detoxification gene families in the evolution process of Aphidinae are different. The comparison of five detoxification gene families among nine Aphidinae species and the estimated relative evolutionary rates provided herein support an understanding of the interaction between and the co-evolution of Aphidinae and plants.

Involvement of chemosensory proteins in host plant searching in the bird cherry-oat aphid

Chemosensory systems are considered to play an important role in host plant selection in herbivorous insects. However, few studies have focused on chemosensory proteins (CSPs) for aphid host-location mechanisms. The roles of CSPs in searching for different Poaceae species (wheat, barley, triticale, maize and sorghum) were tested in Rhopalosiphum padi, an important cereal pest. The olfactometer assays showed that R. padi responds to plant odors. Seven R. padi CSP genes were identified. Influence of aphid morph, tissue and starvation state on expression patterns of CSPs was evaluated. Expression levels of CSP1, CSP4, CSP5 and CSP6 in winged aphids were significantly higher than those in wingless ones. Transcription levels of four genes (CSP1, CSP4, CSP5 and CSP6) were relatively higher in the head with antennae, and the four genes tended to be upregulated following starvation. Silencing of three CSPs (CSP4, CSP5 and CSP6) altered aphid host-location behavior in response to the five different host plants tested. Three volatile compounds of host plants (octanal, [E]-2-hexenol and linalool) have significant attraction to winged R. padi according to the four-arm olfactometer tests. Molecular docking predicted hydrogen bonding sites which played key roles in the binding of CSP4, CSP5 and CSP6 with volatile compounds. Knockdown of CSP4 or CSP5 significantly decreased the staying time of R. padi in the arms with octanal. However, knockdown of CSP6 could not affect the response of R. padi to octanal. These results bring evidence for the involvement of three CSPs in R. padi host-location behavior.

Selection and Validation of Reference Genes For qRT-PCR Analysis of Rhopalosiphum padi (Hemiptera: Aphididae)

Rhopalosiphum padi (L.) (Hemiptera: Aphididae) is an important cosmopolitan pest in cereal crops. Reference genes can significantly affect qRT-PCR results. Therefore, selecting appropriate reference genes is a key prerequisite for qRT-PCR analyses. This study was conducted to identify suitable qRT-PCR reference genes in R. padi. We systematically analyzed the expression profiles of 11 commonly used reference genes. The ΔCt method, the BestKeeper, NormFinder, geNorm algorithms, and the RefFinder online tool were used to evaluate the suitability of these genes under diverse experimental conditions. The data indicated that the most appropriate sets of reference genes were β-actin and GAPDH (for developmental stages), AK and TATA (for populations), RPS18 and RPL13 (for tissues), TATA and GAPDH (for wing dimorphism), EF-1α and RPS6 (for antibiotic treatments), GAPDH and β-actin (for insecticide treatments), GAPDH, TATA, RPS18 (for starvation-induced stress), TATA, RPS6, and AK (for temperatures), and TATA and GAPDH (for all conditions). Our study findings, which revealed the reference genes suitable for various experimental conditions, will facilitate the standardization of qRT-PCR programs, while also improving the accuracy of qRT-PCR analyses, with implications for future research on R. padi gene functions.

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas’ whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.

Genetic Variation May Have Promoted the Successful Colonization of the Invasive Gall Midge, Obolodiplosis robiniae, in China

Invasive species often cause serious economic and ecological damage. Despite decades of extensive impacts of invasives on bio-diversity and agroforestry, the mechanisms underlying the genetic adaptation and rapid evolution of invading populations remain poorly understood. The black locust gall midge, Obolodiplosis robiniae, a highly invasive species that originated in North America, spread widely throughout Asia and Europe in the past decade. Here, we used 11 microsatellite DNA markers to analyze the genetic variation of 22 O. robiniae populations in China (the introduced region) and two additional US populations (the native region). A relatively high level of genetic diversity was detected among the introduced populations, even though they exhibited lower diversity than the native US populations. Evidence for genetic differentiation among the introduced Chinese populations was also found based on the high Fst value compared to the relatively low among the native US populations. Phylogenetic trees, structure graphical output, and principal coordinate analysis plots suggested that the Chinese O. robiniae populations (separated by up to 2,540 km) cluster into two main groups independent of geographical distance. Genetic variation has been observed to increase rapidly during adaptation to a new environment, possibly contributing to population establishment and spread. Our results provide insights into the genetic mechanisms underlying successful invasion, and identify factors that have contributed to colonization by an economically important pest species in China. In addition, the findings improve our understanding of the role that genetic structure plays during invasion by O. robiniae.

Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification

BACKGROUND

Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species.

RESULTS

Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva.

CONCLUSIONS

The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.

Strong genetic differentiation among populations of Cheirotonus gestroi (Coleoptera: Euchiridae) in its native area sheds lights on species conservation

The long-armed scarab (Cheirotonus gestroi) is an endangered large insect in southwestern China and neighboring countries; however, limited information is available regarding its population genetics, hindering conservation efforts. Therefore, we investigated the population genetic structure and evolutionary history of C. gestroi in southwestern China. Twenty-five haplotypes were obtained from 47 specimens across five populations. The Dawei Mountain (DWS) population differed from other populations by a high genetic distance. Population structure analysis generated three distinct clades, corresponding to Hengduan Mountains (HM), Ailao Mountains (AM), and Dawei Mountains (DM), and high-level genetic diversity was found in two HM populations. Collectively, the strong genetic differentiation among populations might be due to limited gene flow, geographical isolation, and habitat fragmentation. Therefore, while developing a conservation strategy, HM, AM, and DM groups should be defined as separate management units. Additionally, the DWS population should be given priority protection due to its uniqueness and low genetic diversity.

Identification and Functional Characterization of Two Sigma Glutathione S-Transferase Genes From Bird Cherry-Oat Aphid (Hemiptera: Aphididae)

The bird cherry-oat aphid, Rhopalosiphum padi (L.), is an insect pest that persistently attacks wheat crops worldwide. Glutathione S-transferases (GSTs) are important detoxification enzymes that play roles in insecticide resistance. In this study, we identified two GST genes (RpGSTS1 and RpGSTS2) from R. padi. Phylogenetic analysis indicated that the genes are associated with the sigma class of insect GSTs. The RpGSTS1 and RpGSTS2 contain nine α-helices and five β-sheets connected by loops, and had 60 and 50% homology with the 3D structure of the Blattella germanica GST5. We tested the toxicity of chlorpyrifos, imidacloprid, isoprocarb, sulfoxaflor, and λ-cyhalothrin to R. padi, and found that the toxicity of five insecticides to the aphid varied. The detoxification activity of GSTs and the expression patterns of RpGSTS1 and RpGSTS2 after insecticide treatments were also analyzed. Compared to the control, the GST activity was increased by 23, 18.5, 13, and 11.5% in aphids treated by LC50 concentrations of chlorpyrifos, isoprocarb, imidacloprid, and sulfoxaflor, respectively. Exposure to different chemical insecticides showed different effects on the expression of RpGSTS1 and RpGSTS2. These results indicate that RpGSTS1 and RpGSTS2 have unique biochemical characteristics and may play roles in resistance to insecticides in R. padi.

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag–simple sequence repeats (EST–SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST–SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.

Functional Analysis of a Carboxylesterase Gene Associated With Isoprocarb and Cyhalothrin Resistance in Rhopalosiphum padi (L.)

Carboxylesterase (CarE) is an important class of detoxification enzymes involved in insecticide resistance. However, the molecular mechanism of CarE-mediated insecticide resistance in Rhopalosiphum padi, a problematic agricultural pest, remains largely unknown. In the present study, an isoprocarb-resistant (IS-R) strain and a cyhalothrin-resistant (CY-R) strain were successively selected from a susceptible (SS) strain of R. padi. The enzyme activity indicated that enhanced carboxylesterase activity contributes to isoprocarb and cyhalothrin resistance. The expression levels of putative CarE genes were examined and compared among IS-R, CY-R, and SS strains, and only the R. padi carboxylesterase gene (RpCarE) was significantly over expressed in both the IS-R and CY-R strains compared to the SS strain. The coding region of the RpCarE gene was cloned and expressed in Escherichia coli. The purified RpCarE protein was able to catalyze the model substrate, α-naphtyl acetate (Kcat = 5.50 s^-1; Km = 42.98 μM). HPLC assay showed that the recombinant protein had hydrolase activity against isoprocarb and cyhalothrin. The modeling and docking analyses consistently indicated these two insecticide molecules fit snugly into the catalytic pocket of RpCarE. Taken together, these findings suggest that RpCarE plays an important role in metabolic resistance to carbamates and pyrethroids in R. padi.

Identification, Expression, and Regulation of an Omega Class Glutathione S-transferase in Rhopalosiphum padi (L.) (Hemiptera: Aphididae) Under Insecticide Stress

Glutathione S-transferases (GSTs) play an essential role in the detoxification of xenobiotic toxins in insects, including insecticides. However, few data are available for the bird cherry-oat aphid, Rhopalosiphum padi (L.). In this study, we cloned and sequenced the full-length cDNA of an omega GST gene (RpGSTO1) from R. padi, which contains 720 bp in length and encodes 239 amino acids. A phylogenetic analysis revealed that RpGSTO1 belongs to the omega class of insect GSTs. RpGSTO1 gene was highly expressed in transformed Escherichia coli and the protein was purified by affinity chromatography. The recombinant RpGSTO1 displayed reduced glutathione (GSH)-dependent conjugating activity toward the substrate 1-chloro-2, 4-dinitrobenzene (CDNB) substrate. The recombinant RpGSTO1 protein exhibited optimal activity at pH 7.0 and 30°C. In addition, a disk diffusion assay showed that E. coli overexpressing RpGSTO1 increased resistance to cumene hydroperoxide-induced oxidative stress. Real-time quantitative PCR analysis showed that the relative expression level of RpGSTO1 was different in response to different insecticides, suggesting that the enzyme could contribute to insecticide metabolism in R. padi. These findings indicate that RpGSTO1 may play a crucial role in counteracting oxidative stress and detoxifying the insecticides. The results of our study contribute to a better understanding the mechanisms of insecticide detoxification and resistance in R. padi.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.