Differential expression analysis of cold tolerance adaptation by RNAseq de novo approach

MENSCH, J; HURTADO, JP; MOREYRA, N; HASSON, E

La Haya

Congreso; 15th European Conference on Computational Biology; 2016

European Society of Computational BIology

<!-- /* Font Definitions */@font-face{font-family:"Liberation Serif";mso-font-alt:"Times New Roman";mso-font-charset:1;mso-generic-font-family:roman;mso-font-pitch:variable;mso-font-signature:0 0 0 0 0 0;}@font-face{font-family:"Droid Sans Fallback";panose-1:0 0 0 0 0 0 0 0 0 0;mso-font-charset:0;mso-generic-font-family:roman;mso-font-format:other;mso-font-pitch:auto;mso-font-signature:0 0 0 0 0 0;}@font-face{font-family:FreeSans;panose-1:0 0 0 0 0 0 0 0 0 0;mso-font-charset:0;mso-generic-font-family:roman;mso-font-format:other;mso-font-pitch:auto;mso-font-signature:0 0 0 0 0 0;} /* Style Definitions */p.MsoNormal, li.MsoNormal, div.MsoNormal{mso-style-unhide:no;mso-style-parent:"";margin:0cm;margin-bottom:.0001pt;mso-pagination:none;mso-hyphenate:none;font-size:12.0pt;font-family:"Liberation Serif","serif";mso-fareast-font-family:"Droid Sans Fallback";mso-bidi-font-family:FreeSans;color:#00000A;mso-fareast-language:ZH-CN;mso-bidi-language:HI;}.MsoChpDefault{mso-style-type:export-only;mso-default-props:yes;font-family:"Liberation Serif","serif";mso-ascii-font-family:"Liberation Serif";mso-fareast-font-family:"Droid Sans Fallback";mso-hansi-font-family:"Liberation Serif";mso-bidi-font-family:FreeSans;mso-fareast-language:ZH-CN;mso-bidi-language:HI;}@page WordSection1{size:612.0pt 792.0pt;margin:70.85pt 3.0cm 70.85pt 3.0cm;mso-header-margin:36.0pt;mso-footer-margin:36.0pt;mso-paper-source:0;}div.WordSection1{page:WordSection1;}-->Over the last years, the role of temperature-related gene expression in ecological adaptation has been receiving increasing attention. Previous findings of our group identified specific cold adaptations involving energy metabolism and arrest of reproduction in females of the fly Drosophila buzzatii in response to winter conditions. We performed a RNA-seq analysis to investigate changes in gene expression profiles in order to identify the genetic basis of such cold adaptations. The study was conducted by exposing sets of females to three thermal conditions: one involving the cold tolerant flies and two control treatments. We used the Trinity software to generate a de novo assembly from RNA-seq reads. To analyze expression levels of the reconstructed transcripts, we mapped the reads against the transcriptome and then estimated the number of RNA-seq fragments (counts) that mapped to each contig. Transcripts were filtered based on a mean count value cutoff and normalized by the TMM method to get the differences in RNA composition. Thereby, we extracted transcripts that were at least 4-fold differentially expressed at a significance of 1E-3 in any comparison. This step allowed us to compare over and under-expression transcript clusters. Based on a well-annotated genome, we made a blastx against D. melanogaster genome. The results showed an over-representation of specific genetic pathways and cellular processes, highlighting the relevance of sugar metabolism, glycolysis and oxidative phosphorylation in the expression of cold tolerance. Future studies will assess the role of natural selection shaping the evolution of differentially expressed genes identified.