Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed
Abstract Background Common 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 ove...
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doaj-e11ff4741c55442aab323ee881c640892020-11-25T03:57:21ZengBMCBMC Genomics1471-21642020-10-0121111310.1186/s12864-020-07099-4Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfedXi Liu0Frédéric Hérault1Christian Diot2Erwan Corre3ABiMS Bioinformatics Facility, CNRS, Sorbonne UniversitéUMR PEGASE, INRAE, Institut AgroUMR PEGASE, INRAE, Institut AgroABiMS Bioinformatics Facility, CNRS, Sorbonne UniversitéAbstract Background Common 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. Results Transcriptomes 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. Conclusions Analyses 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.http://link.springer.com/article/10.1186/s12864-020-07099-4RNA sequencingInterspecific hybridsDe novo transcriptome assemblyGene expressionLiver steatosis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xi Liu Frédéric Hérault Christian Diot Erwan Corre |
spellingShingle |
Xi Liu Frédéric Hérault Christian Diot Erwan Corre Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed BMC Genomics RNA sequencing Interspecific hybrids De novo transcriptome assembly Gene expression Liver steatosis |
author_facet |
Xi Liu Frédéric Hérault Christian Diot Erwan Corre |
author_sort |
Xi Liu |
title |
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
title_short |
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
title_full |
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
title_fullStr |
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
title_full_unstemmed |
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
title_sort |
development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-10-01 |
description |
Abstract Background Common 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. Results Transcriptomes 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. Conclusions Analyses 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. |
topic |
RNA sequencing Interspecific hybrids De novo transcriptome assembly Gene expression Liver steatosis |
url |
http://link.springer.com/article/10.1186/s12864-020-07099-4 |
work_keys_str_mv |
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