Transcriptomics to identify colour pattern genes
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR696684.fastq.gz | Fastqsanger.gz | |||
| ERR696684_1.fastq.gz | Fastqsanger.gz | |||
| ERR696684_2.fastq.gz | Fastqsanger.gz | |||
| ERR698971.fastq.gz | Fastqsanger.gz | |||
| ERR698971_1.fastq.gz | Fastqsanger.gz |
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Project description:We use RNAseq data to perform differential gene expression to identify genes controlling structural colouration in two co-mimetic species of Heliconius butterfly - Heliconius erato and Heliconius melpomene. We use comparisons between iridescent and non-iridescent subspecies of Helcionius erato (H. e. cyrbia and H. e. demophoon, respectively) and Helcionius melpomene (H. m. cythera and H. m. rosina, respectively) at two separate developmental stages, 50% and 70% of development. In addition, in the iridescent subspecies of both H. erato and H. melpomene, we compared the iridescent wing regions (forewing and hindwing combined) to the non-iridescent androconial wing region using differential gene expression.
2021-12-10 | GSE190378 | GEO
Project description:We use RNAseq data to perform differential gene expression analysis to identify genes controlling structural colouration in two co-mimetic species of Heliconius butterfly - Heliconius erato and Heliconius melpomene. We use comparisons between iridescent and non-iridescent subspecies of Helcionius erato (H. e. cyrbia and H. e. demophoon, respectively) and Helcionius melpomene (H. m. cythera and H. m. rosina, respectively) at two separate developmental stages, 50% and 70% of development. In addition, in the iridescent subspecies of both H. erato and H. melpomene, we compared the iridescent wing regions (forewing and hindwing combined) to the non-iridescent androconial wing (anterior hindwing) region using differential gene expression.
2021-12-10 | GSE190379 | GEO
Project description:Background: Heliconius butterflies are an excellent model system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus and several genes in this region show expression pattern differences across races. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. It seems likely that miRNAs could act as downstream regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs appeared to be differentially expressed between colour pattern races and this was tested further in different developing pupal wing stages using Northern blots. These revealed that differences in expression were due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified miR-193 and miR-2788; located 2380bp apart in an intergenic region. A search for miRNAs in all available H. melpomene BAC sequences (~2.5Mb) did not reveal any other miRNA genes and no novel miRNAs were predicted. There were several regions where other small RNA sequences assembled to the HmYb region and appeared to be differentially expressed.These might represent other regulatory RNAs. Conclusions: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages. Two miRNAs were located in the HmYb region. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes. High-throughput sequencing of Heliconius melpomene endogenous small RNAs. Size fractionated small RNA from total RNA extracts of two different Heliconius melpomene races (Heliconius melpomene melpomene and Heliconius melpomene rosina) were isolated from wing tissue using miRVana kit. 100µg RNA from 11 individuals of different developmental stages was pooled for each race as follows: 4.1% larval stage <1; 2% larval stage 1-1.75; 2.9% larval stage 2-2.5; 22% larval stage 2.75-3; 19% larval stage > 3; 25% early pupae; 25% mid-melanin pupae. Sequences were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
2011-06-02 | E-GEOD-23292 | biostudies-arrayexpress
Project description:Background: Heliconius butterflies are an excellent model system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus and several genes in this region show expression pattern differences across races. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. It seems likely that miRNAs could act as downstream regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs appeared to be differentially expressed between colour pattern races and this was tested further in different developing pupal wing stages using Northern blots. These revealed that differences in expression were due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified miR-193 and miR-2788; located 2380bp apart in an intergenic region. A search for miRNAs in all available H. melpomene BAC sequences (~2.5Mb) did not reveal any other miRNA genes and no novel miRNAs were predicted. There were several regions where other small RNA sequences assembled to the HmYb region and appeared to be differentially expressed.These might represent other regulatory RNAs. Conclusions: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages. Two miRNAs were located in the HmYb region. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.
2011-06-02 | GSE23292 | GEO
Project description:Aposematic color pattern mimicry in Heliconius butterflies provides a well-known example of adaptation via selection on a few genes of large effect. To understand how selection at individual genes can drive the evolution of complex traits, we functionally characterized five novel enhancers of the color pattern gene, optix. In Heliconius erato we found that wing pattern enhancers are largely ancestral, pleiotropic, functionally interdependent, and introgressed between populations. Remarkably, many of these enhancers are also associated with regional pattern variation in the distantly related co-mimics Heliconius melpomene and Heliconius timareta. Our findings provide a case study of how parallel co-evolution of ancient, multifunctional regulatory elements can facilitate the rapid diversification of complex phenotypes, and provide a counterpoint to many widespread assumptions of cis-regulatory evolution.
2021-06-04 | GSE123703 | GEO
Project description:Aposematic color pattern mimicry in Heliconius butterflies provides a well-known example of adaptation via selection on a few genes of large effect. To understand how selection at individual genes can drive the evolution of complex traits, we functionally characterized five novel enhancers of the color pattern gene, optix. In Heliconius erato we found that wing pattern enhancers are largely ancestral, pleiotropic, functionally interdependent, and introgressed between populations. Remarkably, many of these enhancers are also associated with regional pattern variation in the distantly related co-mimics Heliconius melpomene and Heliconius timareta. Our findings provide a case study of how parallel co-evolution of ancient, multifunctional regulatory elements can facilitate the rapid diversification of complex phenotypes, and provide a counterpoint to many widespread assumptions of cis-regulatory evolution.
2021-06-04 | GSE123701 | GEO
Project description:Aposematic color pattern mimicry in Heliconius butterflies provides a well-known example of adaptation via selection on a few genes of large effect. To understand how selection at individual genes can drive the evolution of complex traits, we functionally characterized five novel enhancers of the color pattern gene, optix. In Heliconius erato we found that wing pattern enhancers are largely ancestral, pleiotropic, functionally interdependent, and introgressed between populations. Remarkably, many of these enhancers are also associated with regional pattern variation in the distantly related co-mimics Heliconius melpomene and Heliconius timareta. Our findings provide a case study of how parallel co-evolution of ancient, multifunctional regulatory elements can facilitate the rapid diversification of complex phenotypes, and provide a counterpoint to many widespread assumptions of cis-regulatory evolution.
2021-06-04 | GSE123700 | GEO
Project description:Comparison of whole genome and tiled gene expression between different colour pattern races of H. melpomene in developing wings.
2015-03-31 | GSE64051 | GEO
Project description:The genetic basis of structural colour variation in mimetic Heliconius butterflies [melpomene]
| PRJNA786906 | ENA
Project description:We made RNA-Seq libraries of Heliconius melpomene heads, antennae, legs and mouth parts to identify genes upregulated in heads. We explored the expression patterns of a gene family that functions in visual pigment chromophore transport in Drosophila to identify a non-orthologous gene that has a similar function.
2018-02-28 | E-MTAB-6342 | biostudies-arrayexpress