S+JRA7.2MfNinsects
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ABSTRACT:
PROVIDER: PRJEB59182 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development.
2016-07-27 | GSE71990 | GEO
Project description:All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. We found abundant small RNAs and their different expression profiles in the two phases.
2009-01-16 | GSE12640 | GEO
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development. Chromatin Immunoprecipitation (ChIP) was used to identify genome wide targets bound by Ubx in Bombyx larval wing buds. The experiment to enrich Ubx bound regions was carried out using a Bombyx N terminal-Ubx specific poylclonal antibody raised in Rabbit and purified against a Protein A column to obtain IgG fraction. An Immunoprecipitation (IP) with Normal Rabbit IgG was used as a negative control to eliminate the regions that pertained to non specific binding to an Immunogloubulin. The normalization of both ChIP and IgG was done against sequenced input chromatin. Two replicates of single end 36 bp reads were sequenced using Ilumina for all the three conditions and for both fore and hind wing tissue samples.The peaks common to both the replicates were considered after applying a FDR cutoff.The fore wing target set was used for comparison with the hind wing targets.
2016-07-27 | E-GEOD-71990 | biostudies-arrayexpress
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis.To understand the differential development of wing appendages in insects we intend to compare the differential expression of fore and hind wing appendages in Diptera and Lepidoptera. We have employed RNA-seq using by illumina sequencing to identify the genes that are differentially expressed between fore and the hind wing bud of the Bombyx larvae. Only one replicate was performed as the intended study was to validate the differential targets in comparison to ChIP studies and other methods of select candidates. Total RNA was extarcted from wing buds of IV instar Bombyx larvae and sequenced on an illumina sequencer. Wing buds were collected directly in liquid nitrogen and 80 such buds each for fore and hind wing were collected from IV instar larvae. RNA was isolated from them and processed for Library preperation and illumina sequencing. One replicate was done as a supplement to ChIP studies.
2016-07-27 | E-GEOD-71988 | biostudies-arrayexpress
Project description:DNA methylation is an important chromatin modification that is necessary for the structural integrity and proper regulation of the genome for many species. Despite its conservation across the tree of life, little is known about its contribution to complex traits. Reports that differences in DNA methylation between castes in closely related Hymenopteran insects (ants, bees and wasps) contributes to social behaviors has generated hypotheses on the role of DNA methylation in governing social behavior. However, social behavior has evolved multiple times across insecta, and a common role of DNA methylation in social behavior remains outstanding. Using phylogenetic comparative methods we sought to better understand patterns of DNA methylation and social behavior across insects. DNA methylation can be found in social and solitary insects from all orders, except Diptera (flies), which suggests a shared loss of DNA methylation within this order. The lack of DNA methylation is reflected in the absence of the maintenance and de novo DNA methyltransferases (DNMT) 1 and 3, respectively. Interestingly, DNA methylation is found in species without DNMT3. DNA methylation and social behavior (social/solitary) or with division of labor (caste+/caste–) for 123 insect species analyzed from 11 orders are not evolutionary dependent, which is further supported by sequencing of DNA methylomes from 40 species.
2017-02-02 | GSE83497 | GEO
Project description:The most common ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reproductive ability. In this study, we collected female adults in three different states, i.e., non-diapause, diapause and diapause termination, for transcriptome sequencing. The experimental insects consisted of three different states as follows: Non-diapause female insects were reared at 24±1°C, with a RH of 70±10% and a 16:8 h light: dark (L: D) photoperiod and collected after their first oviposition. Female adults in diapause were reared at 18±1°C at an RH of 70±10% and a 10:14-h (L:D) photoperiod. The experimental diapause insects were collected after 30 days. Diapause-terminated adults were transferred to another climatic cabinet with the 30-day diapause insects and reared under the same conditions as the non-diapause insects. After their first oviposition, the female insects were collected and stored at -80°C. Three biological replicates per treatment (non-diapause, diapause, diapause-terminated) were sequenced using Illumina HiSeq 2500.
2016-06-01 | E-GEOD-75645 | biostudies-arrayexpress
Project description:During the over 300 million years of co-evolution between herbivorous insects and their host plants, a dynamic equilibrium of evolutionary arms race has been established. However, the co-adaptation between insects and their host plants is a complex process, often driven by multiple evolutionary mechanisms. We found that various lepidopteran pests that use maize as a host exhibit differential adaptation to the plant secondary metabolites, benzoxazinoids (BXs). Notably, the Spodoptera genus, including Spodoptera frugiperda (fall armyworm) and Spodoptera litura (cotton leafworm), demonstrate greater tolerance to BXs compared to other insects. Through comparative transcriptomic analysis of the midgut, we identified four candidate genes potentially involved in BXs detoxification in S. frugiperda. Subsequently, we confirmed two UGT genes, Sfru33T10 and Sfru33F32, as key players in BXs detoxification using CRISPR/Cas9 gene-editing technology. Phylogenetic analysis revealed that Sfru33T10 evolved independently within the Noctuidae family and is involved in the glycosylation of HDMBOA, while Sfru33F32 evolved independently within the Spodoptera genus and functions as a key detoxification enzyme responsible for the glycosylation of both DIMBOA and HMBOA. Our study demonstrates that the UGT gene family plays a crucial role in the adaptation of noctuid insects to maize, with multiple independent evolutionary events within the Noctuidae family and the Spodoptera genus contributing significantly to host adaptation.
2024-09-18 | GSE276946 | GEO
Project description:All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. We found abundant small RNAs and their different expression profiles in the two phases. Small RNAs were sequenced from gregarious and solitary phases of Locusta migratoria,respectively.
2009-01-16 | E-GEOD-12640 | biostudies-arrayexpress
Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis.To understand the differential development of wing appendages in insects we intend to compare the differential expression of fore and hind wing appendages in Diptera and Lepidoptera. We have employed RNA-seq using by illumina sequencing to identify the genes that are differentially expressed between fore and the hind wing bud of the Bombyx larvae. Only one replicate was performed as the intended study was to validate the differential targets in comparison to ChIP studies and other methods of select candidates.
2016-07-27 | GSE71988 | GEO
Project description:The olfactory system is intricately intertwined with species adaptation in insects. Genomic studies have unveiled significant duplications and expansions of olfactory receptor genes in social behavior insects. However, the precise mechanisms through which these duplicated genes integrate into olfactory neural circuitries to enhance species-specific adaptative functions remain inadequately understood.
2025-04-23 | GSE248096 | GEO