InsectBase: a resource for insect genomes and transcriptomes

Yin, Chuanlin; Gengyu, Shen; Guo, Dan; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan; Liu, Ying; Yiqun, Zhang; Yu, Kaixiang; Huang, Shuiqing; Li, Fēi

doi:10.1093/nar/gkv1204

Cited by 139 publications

(121 citation statements)

References 34 publications

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“…Three novel expressed sequence tags corresponding to three novel alp transcripts were obtained from the C . suppressalis transcriptome obtained in previous studies (Ma et al ., ; Wang et al ., ; Yin et al ., ). A smart rapid amplification of cDNA ends (RACE) cDNA amplification kit (Takara, Kyoto, Japan) was used to amplify the ORFs of three Csalp genes, and pairs of gene‐specific primers were designed based on the partial sequences using P rimer 5.0 software (Supporting Information Table S1) (Qiu et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines

Qiu

Wang

et al. 2017

Insect Molecular Biology

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Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis are highly toxic to lepidopteran pests. Strains of transgenic rice expressing cry genes have been developed that are resistant to rice pests. Understanding the mode of action of Cry toxins in rice pests will improve our ability to use them effectively as insecticides. In this study, we tested the hypothesis that alkaline phosphatases (ALPs) are involved in Cry1A, Cry2Aa and Cry1Ca toxicity in Chilo suppressalis, an important insect pest of rice crops in China. We first cloned three novel C. suppressalis alps (Csalps) from the larval midgut of C. suppressalis. RNA interference knockdown of six different Csalp genes (Csalp1, Csalp2, Csalp3, Csalp4, Csalp5 and Csalp6) showed that knockdown of three of these, Csalp1, Csalp2 and Csalp4, reduced larval mortality to the transgenic rice strain TT51, which expresses a fusion protein of Cry1Ab and Cry1Ac, whereas suppression of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp6 transcripts decreased the susceptibility of larvae to the transgenic rice strain T2A-1, which expresses cry2Aa.Moreover, downregulation of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp5 transcripts conferred significant tolerance to the transgenic rice strain T1C-19, which expresses cry1Ca. These results suggest that these ALPs play a key role in the toxicity of Cry1A, Cry2A and Cry1C to C. suppressalis.

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Section: Methodsmentioning

confidence: 97%

Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines

Qiu

Wang

et al. 2017

Insect Molecular Biology

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“…Chromatin-based regulatory data can also be found in many of the major model organism databases and through genomics projects such as ENCODE and modENCODE [39, 40]. Although they currently do not include regulatory data, annotated insect genomes can be accessed through the National Agricultural Library’s i5k Workspace (56 genomes)[41] and InsectBase (138 genomes)[42], providing a potentially rich source for comparative genomic analyses. Overall, however, comprehensively annotated regulatory genomes remain frustratingly lacking, and the need for CRM identification presents a major stumbling block for extensive GRN characterization and studies of GRN evolution.…”

Section: Genomes and Regulatory Annotationmentioning

confidence: 99%

Perspectives on Gene Regulatory Network Evolution

Halfon

2017

Trends in Genetics

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Animal development proceeds through the activity of genes and their cis-regulatory modules, working together in sets of gene regulatory networks (GRNs). Emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here different aspects of GRN evolution and argue that developmental system drift, in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution. Advances in methods to discover related cis-regulatory modules in diverse insect species, a critical requirement for detailed GRN characterization, are also described.

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“…We developed a Perl script to identify the 3 ′ UTR sequences using transcriptome and genome data, which were deposited in InsectBase (www.insect-genome.com) (Yin et al 2016). The coding region of assembled transcripts was first predicted using TransDecoder with the default parameters.…”

Section: Mirna Target Predictionmentioning

confidence: 99%

Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis

Sun

Xiao

et al. 2017

RNA

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The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of suppressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dualluciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titer of 20-hydroxyecdysone (20E), induced mortality, and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity.

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InsectBase: a resource for insect genomes and transcriptomes

Cited by 139 publications

References 34 publications

Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines

Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines

Perspectives on Gene Regulatory Network Evolution

Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis

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