Abstract
BackgroundCommon Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from different species and comparison is challenging. The goal of this study was develop a relevant strategy for transcriptome analysis and comparison between different species.ResultsTranscriptomes were first assembled with a reference-based approach. Important mapping biases were observed when heterologous mapping were conducted on common duck reference genome, suggesting that this reference-based strategy was not suited to compare the four different genetic types. De novo transcriptome assemblies were then performed using Trinity and Oases. Assemblies of transcriptomes were not relevant when more than a single genetic type was considered. Finally, single genetic type transcriptomes were assembled with DRAP in a mega-transcriptome. No bias was observed when reads from the different genetic types were mapped on this mega-transcriptome and differences in gene expression between the four genetic types could be identified.ConclusionsAnalyses using both reference-based and de novo transcriptome assemblies point out a good performance of the de novo approach for the analysis of gene expression in different species. It also allowed the identification of differences in responses to overfeeding between Pekin and Muscovy ducks and hinny and mule hybrids.
Highlights
Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production
Heterologous mapping rate of Muscovy and to a lesser extend of Hinny and Mule transcriptomes (40, 58, 59%, respectively) were lower than homologous mapping rate of Pekin transcriptome (71%) on this common duck reference genome, clearly indicating an important bias in heterologous mapping when compared to homologous mapping
De novo transcriptome assemblies After adapters removing, quality trimming and filtering of reads, 545,691,171, 504,591,419, 534,967,150 and 627, 575,995 pairs were conserved for Pekin, Muscovy, Hinny and Mule ducks, respectively
Summary
Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. Liver steatosis can occur spontaneously as a result of energy storage before migration This natural ability has been exploited for thousand years to produce fatty liver or “foie gras” by overfeeding ducks or geese in a short period of time. Some studies have been conducted to better characterize hepatic steatosis development in waterfowls and analyze differences between genotypes. They mainly focused on biochemical levels [1,2,3,4,5]. Genome-wide analyses of gene expression are still needed to better characterize hepatic steatosis in ducks and their hybrids
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
