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De novo sequencing, assembly and characterization of antennal transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae).

Chen H, Lin L, Xie M, Zhang G, Su W - PLoS ONE (2014)

Bottom Line: We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection.We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China.

ABSTRACT

Background: Anomala corpulenta is an important insect pest and can cause enormous economic losses in agriculture, horticulture and forestry. It is widely distributed in China, and both larvae and adults can cause serious damage. It is difficult to control this pest because the larvae live underground. Any new control strategy should exploit alternatives to heavily and frequently used chemical insecticides. However, little genetic research has been carried out on A. corpulenta due to the lack of genomic resources. Genomic resources could be produced by next generation sequencing technologies with low cost and in a short time. In this study, we performed de novo sequencing, assembly and characterization of the antennal transcriptome of A. corpulenta.

Results: Illumina sequencing technology was used to sequence the antennal transcriptome of A. corpulenta. Approximately 76.7 million total raw reads and about 68.9 million total clean reads were obtained, and then 35,656 unigenes were assembled. Of these unigenes, 21,463 of them could be annotated in the NCBI nr database, and, among the annotated unigenes, 11,154 and 6,625 unigenes could be assigned to GO and COG, respectively. Additionally, 16,350 unigenes could be annotated in the Swiss-Prot database, and 14,499 unigenes could map onto 258 pathways in the KEGG Pathway database. We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection. We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.

Conclusion: We produced the first large-scale antennal transcriptome of A. corpulenta, which is a species that has little genomic information in public databases. The identified chemodetection unigenes can promote the molecular mechanistic study of behavior in A. corpulenta. These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

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Related in: MedlinePlus

Alignment of amino acid sequences of OBPs (A) and CSPs (B) from A. corpulenta.Conserved residues were highlighted in gray and conserved cysteines were marked with “*” below the alignment.
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pone-0114238-g009: Alignment of amino acid sequences of OBPs (A) and CSPs (B) from A. corpulenta.Conserved residues were highlighted in gray and conserved cysteines were marked with “*” below the alignment.

Mentions: Considering that chemodetection plays a key role in insect behavior, and determination of the specific genes involved in the pathway of odorant detection could be beneficial for control of A. corpulenta adults, we analyzed the unigenes related to chemodetection. The unigenes related to ORs (odorant receptors, olfactory receptors and chemosensory receptors), OBPs (odorant binding receptors), PBPs (pheromone binding proteins), CSPs (chemosensory proteins), PDEs (pheromone degrading enzymes), SNMPs (sensory neuron membrane proteins) and SAPs (sensory appendage proteins) were identified (Table 2). There were 93 related unigenes obtained for ORs, 24 for OBPs, 7 for PBPs and 6 for CSPs, and, in total, 167 unigenes’ functions were related to chemodetection. In this study, we detected 24 OBPs unigenes and 6 CSPs unigenes. Nilaparvata lugens antenna transcriptome contained 10 OBPs and 11 CSPs [36], while for the T. castaneum genome which is the only known genomic sequence in the Coleoptera, has 19 CSPs and 19 OBPs. The OBPs we obtained from A. corpulenta antenna is a little more than in T. castaneum, but the number of CSPs is much less than in T. castaneum. This may indicate the CSPs have more functions beside chemodetection and exist in tissues other than the antenna. According to the unigenes’ sequences, we identified 4 OBPs and 3 CSPs’ full length cDNAs sequence (Table 3). The nucleotide sequences and deduced amino acid sequences are shown in Figure S2 in Data S1, and some traits of nucleotide and putative amino acid sequences of OBPs and CSPs are shown in Table S4 in Data S1. Alignment of OBPs and CSPs are shown in figure 9, and the alignment results show all OBPs from A. corpulenta have six cysteine residues conserved [37] and all CSPs have four cysteine residues conserved [38]. In OBPs, the function of six cysteine residues were considered to constitute three disulfide bridges, to further protect and bind small hydrophobic ligands [39], [40].


De novo sequencing, assembly and characterization of antennal transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae).

Chen H, Lin L, Xie M, Zhang G, Su W - PLoS ONE (2014)

Alignment of amino acid sequences of OBPs (A) and CSPs (B) from A. corpulenta.Conserved residues were highlighted in gray and conserved cysteines were marked with “*” below the alignment.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4252136&req=5

pone-0114238-g009: Alignment of amino acid sequences of OBPs (A) and CSPs (B) from A. corpulenta.Conserved residues were highlighted in gray and conserved cysteines were marked with “*” below the alignment.
Mentions: Considering that chemodetection plays a key role in insect behavior, and determination of the specific genes involved in the pathway of odorant detection could be beneficial for control of A. corpulenta adults, we analyzed the unigenes related to chemodetection. The unigenes related to ORs (odorant receptors, olfactory receptors and chemosensory receptors), OBPs (odorant binding receptors), PBPs (pheromone binding proteins), CSPs (chemosensory proteins), PDEs (pheromone degrading enzymes), SNMPs (sensory neuron membrane proteins) and SAPs (sensory appendage proteins) were identified (Table 2). There were 93 related unigenes obtained for ORs, 24 for OBPs, 7 for PBPs and 6 for CSPs, and, in total, 167 unigenes’ functions were related to chemodetection. In this study, we detected 24 OBPs unigenes and 6 CSPs unigenes. Nilaparvata lugens antenna transcriptome contained 10 OBPs and 11 CSPs [36], while for the T. castaneum genome which is the only known genomic sequence in the Coleoptera, has 19 CSPs and 19 OBPs. The OBPs we obtained from A. corpulenta antenna is a little more than in T. castaneum, but the number of CSPs is much less than in T. castaneum. This may indicate the CSPs have more functions beside chemodetection and exist in tissues other than the antenna. According to the unigenes’ sequences, we identified 4 OBPs and 3 CSPs’ full length cDNAs sequence (Table 3). The nucleotide sequences and deduced amino acid sequences are shown in Figure S2 in Data S1, and some traits of nucleotide and putative amino acid sequences of OBPs and CSPs are shown in Table S4 in Data S1. Alignment of OBPs and CSPs are shown in figure 9, and the alignment results show all OBPs from A. corpulenta have six cysteine residues conserved [37] and all CSPs have four cysteine residues conserved [38]. In OBPs, the function of six cysteine residues were considered to constitute three disulfide bridges, to further protect and bind small hydrophobic ligands [39], [40].

Bottom Line: We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection.We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China.

ABSTRACT

Background: Anomala corpulenta is an important insect pest and can cause enormous economic losses in agriculture, horticulture and forestry. It is widely distributed in China, and both larvae and adults can cause serious damage. It is difficult to control this pest because the larvae live underground. Any new control strategy should exploit alternatives to heavily and frequently used chemical insecticides. However, little genetic research has been carried out on A. corpulenta due to the lack of genomic resources. Genomic resources could be produced by next generation sequencing technologies with low cost and in a short time. In this study, we performed de novo sequencing, assembly and characterization of the antennal transcriptome of A. corpulenta.

Results: Illumina sequencing technology was used to sequence the antennal transcriptome of A. corpulenta. Approximately 76.7 million total raw reads and about 68.9 million total clean reads were obtained, and then 35,656 unigenes were assembled. Of these unigenes, 21,463 of them could be annotated in the NCBI nr database, and, among the annotated unigenes, 11,154 and 6,625 unigenes could be assigned to GO and COG, respectively. Additionally, 16,350 unigenes could be annotated in the Swiss-Prot database, and 14,499 unigenes could map onto 258 pathways in the KEGG Pathway database. We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection. We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.

Conclusion: We produced the first large-scale antennal transcriptome of A. corpulenta, which is a species that has little genomic information in public databases. The identified chemodetection unigenes can promote the molecular mechanistic study of behavior in A. corpulenta. These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

Show MeSH
Related in: MedlinePlus