P0115RNA-Seq Data Challenges for Novel Drosophila Species
RNA-Seq Data Challenges for Novel Drosophila Species
Drosophila melanogaster is one of the most widely studied invertebrates, but fruit flies are a large group with a lot of variation among its members. Drosophila funebris is a novel species that is a distant relative of melanogaster. There is currently no draft genome for funebris, so as a first-pass analysis of its genome, we will delve into transcriptomics to find differences between this species and its rock star cousin.
The main interest for this project is in abdominal pigmentation and the genes that control it. Samples were collected from pupal abdominal epidermis tissue in triplicate from males and females o funebris and melanogaster for a total of 12 samples. Sequencing was done at Tufts Core Facility using Illumina Rapid 150 bp paired-end libraries.
Reads were trimmed, filtered, and normalized before being combined in a co-assembly with Trinity. The resulting gene models were analyzed for differential expression using RSEM and EdgeR. Yellow and tan were identified among the differentially expressed genes between the sexes. The signal for differential expression was higher between the sexes than between the Drosophila species. The Trinotate pipeline was used to create a rough annotation for the gene models. In this poster, the pipeline is presented along with the results and a description of various obstacles and how they were overcome.
The main interest for this project is in abdominal pigmentation and the genes that control it. Samples were collected from pupal abdominal epidermis tissue in triplicate from males and females o funebris and melanogaster for a total of 12 samples. Sequencing was done at Tufts Core Facility using Illumina Rapid 150 bp paired-end libraries.
Reads were trimmed, filtered, and normalized before being combined in a co-assembly with Trinity. The resulting gene models were analyzed for differential expression using RSEM and EdgeR. Yellow and tan were identified among the differentially expressed genes between the sexes. The signal for differential expression was higher between the sexes than between the Drosophila species. The Trinotate pipeline was used to create a rough annotation for the gene models. In this poster, the pipeline is presented along with the results and a description of various obstacles and how they were overcome.