干旱区生态环境知识资源中心(Arid): 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

Arid

DOI	10.1186/s12864-020-07099-4
	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
	Liu, Xi; Herault, Frederic; Diot, Christian; Corre, Erwan
通讯作者	Corre, E
来源期刊	BMC GENOMICS
ISSN	1471-2164
出版年	2020
卷号	21 期号:1
英文摘要	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.
英文关键词	RNA sequencing Interspecific hybrids De novo transcriptome assembly Gene expression Liver steatosis
类型	Article
语种	英语
开放获取类型	gold, Green Published, Green Submitted
收录类别	SCI-E
WOS记录号	WOS:000576983800004
WOS关键词	RNA-SEQ DATA ; GENE-EXPRESSION ; HEPATIC STEATOSIS ; DIFFERENTIAL GENE ; LIPID SECRETION ; LIVER LIPIDS ; SUSCEPTIBILITY ; ANNOTATION ; GENERATION ; PACKAGE
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/326736
作者单位	[Liu, Xi; Corre, Erwan] Sorbonne Univ, ABiMS Bioinformat Facil, CNRS, FR2424,Stn Biol, F-29680 Roscoff, France; [Herault, Frederic; Diot, Christian] INRAE, UMR PEGASE, Inst Agro, 16 Le Clos, F-35590 St Gilles, France
推荐引用方式 GB/T 7714	Liu, Xi,Herault, Frederic,Diot, Christian,et al. 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[J],2020,21(1).
APA	Liu, Xi,Herault, Frederic,Diot, Christian,&Corre, Erwan.(2020).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,21(1).
MLA	Liu, Xi,et al."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 21.1(2020).