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Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests.

Noda H, Kawai S, Koizumi Y, Matsui K, Zhang Q, Furukawa S, Shimomura M, Mita K - BMC Genomics (2008)

Bottom Line: An EST database is available at our web site.The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH.Moreover, specific genes for hemimetabolous insects will be identified.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan. hnada@affrc.go.jp

ABSTRACT

Background: The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background.

Results: More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site.

Conclusion: The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.

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Homology of planthopper ESTs with three insect species by BLASTX. All 37,122 ESTs were examined against protein databases of Apis mellifera, Anopheles gambiae, and Drosophila melanogaster. The ratios of the EST clones are shown based on the e-value in the annotation description of BLASTX.
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Figure 9: Homology of planthopper ESTs with three insect species by BLASTX. All 37,122 ESTs were examined against protein databases of Apis mellifera, Anopheles gambiae, and Drosophila melanogaster. The ratios of the EST clones are shown based on the e-value in the annotation description of BLASTX.

Mentions: Insects are a large group among animals and are quite divergent. Many ESTs of BPH showed no homology in the nucleotide and amino acid sequences. To examine the similarity level of the genes among insect species, we conducted homology searches using BLASTX against protein data of three insect species, Drosophila melanogaster, Anopheles gambiae, and Apis mellifera. All 37,122 ESTs were examined against each protein database, and were grouped by the e-value shown in the BLAST result (Fig. 9). Of ESTs, 35–40% showed homology with the proteins of the three insect species with <e-30, but 35–40% showed very little or no homology with the proteins of the three insects. Some genes showing 'no homology' or 'no-hit-found' might be those that are not translated into proteins. It is worth consideration that BPH is a hemimetabolous insect, which has no pupal stage, and the other three species are holometabolous ones. This difference might affect the low homology between them.


Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests.

Noda H, Kawai S, Koizumi Y, Matsui K, Zhang Q, Furukawa S, Shimomura M, Mita K - BMC Genomics (2008)

Homology of planthopper ESTs with three insect species by BLASTX. All 37,122 ESTs were examined against protein databases of Apis mellifera, Anopheles gambiae, and Drosophila melanogaster. The ratios of the EST clones are shown based on the e-value in the annotation description of BLASTX.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2311293&req=5

Figure 9: Homology of planthopper ESTs with three insect species by BLASTX. All 37,122 ESTs were examined against protein databases of Apis mellifera, Anopheles gambiae, and Drosophila melanogaster. The ratios of the EST clones are shown based on the e-value in the annotation description of BLASTX.
Mentions: Insects are a large group among animals and are quite divergent. Many ESTs of BPH showed no homology in the nucleotide and amino acid sequences. To examine the similarity level of the genes among insect species, we conducted homology searches using BLASTX against protein data of three insect species, Drosophila melanogaster, Anopheles gambiae, and Apis mellifera. All 37,122 ESTs were examined against each protein database, and were grouped by the e-value shown in the BLAST result (Fig. 9). Of ESTs, 35–40% showed homology with the proteins of the three insect species with <e-30, but 35–40% showed very little or no homology with the proteins of the three insects. Some genes showing 'no homology' or 'no-hit-found' might be those that are not translated into proteins. It is worth consideration that BPH is a hemimetabolous insect, which has no pupal stage, and the other three species are holometabolous ones. This difference might affect the low homology between them.

Bottom Line: An EST database is available at our web site.The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH.Moreover, specific genes for hemimetabolous insects will be identified.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan. hnada@affrc.go.jp

ABSTRACT

Background: The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background.

Results: More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site.

Conclusion: The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.

Show MeSH
Related in: MedlinePlus