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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Liu X,Hérault F,Diot C,Corre Edoi
10.1186/s12864-020-07099-4subject
Has Abstractpub_date
2020-10-02 00:00:00pages
687issue
1issn
1471-2164pii
10.1186/s12864-020-07099-4journal_volume
21pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-58
更新日期:2012-02-03 00:00:00
abstract:BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-627
更新日期:2012-11-15 00:00:00
abstract:BACKGROUND:Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultrasound images affect the post-processing, such as follicle segmentation and finally affect the measur...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S2-S9
更新日期:2010-11-02 00:00:00
abstract:BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-720
更新日期:2012-12-22 00:00:00
abstract:BACKGROUND:The transcriptome of the fruit pulp of the sweet orange variety Anliu (WT) and that of its red fleshed mutant Hong Anliu (MT) were compared to understand the dynamics and differential expression of genes expressed during fruit development and ripening. RESULTS:The transcriptomes of WT and MT were sampled at...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-10
更新日期:2012-01-10 00:00:00
abstract:BACKGROUND:The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce. RESULTS:We introduce CLA...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1419-2
更新日期:2015-03-25 00:00:00
abstract:BACKGROUND:Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism has been key to the evolution of the Hymenoptera, and particularly the social Hymenoptera where the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-623
更新日期:2011-12-20 00:00:00
abstract:BACKGROUND:The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identificati...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-16
更新日期:2012-01-11 00:00:00
abstract:BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-9-630
更新日期:2008-12-23 00:00:00
abstract:BACKGROUND:As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout (Oncorhynchus mykiss gairdneri) that have evolved...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1246-5
更新日期:2015-02-21 00:00:00
abstract:BACKGROUND:High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integrat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-514
更新日期:2013-07-29 00:00:00
abstract:BACKGROUND:Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4967-4
更新日期:2018-08-06 00:00:00
abstract:BACKGROUND:Major changes in gene expression occur in the fetal brain to modulate the function of this organ postnatally. Thus, factors can alter the genomics of the fetal brain, predisposing to neurological disorders later in life. We hypothesized that the physiological dynamics of the immune system transcriptome of th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1001
更新日期:2014-11-19 00:00:00
abstract:BACKGROUND:Cytochrome P450s (CYPs) in animals fall into two categories: those that synthesize or metabolize endogenous molecules and those that interact with exogenous chemicals from the diet or the environment. The latter form a critical component of detoxification systems. RESULTS:Data mining and manual curation of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-169
更新日期:2009-04-21 00:00:00
abstract:BACKGROUND:Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5137-4
更新日期:2018-11-06 00:00:00
abstract:BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5467-x
更新日期:2019-04-04 00:00:00
abstract:BACKGROUND:Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic anal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-517
更新日期:2012-10-01 00:00:00
abstract:BACKGROUND:After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-63
更新日期:2011-01-26 00:00:00
abstract:BACKGROUND:The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 ta...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-370
更新日期:2008-08-01 00:00:00
abstract:BACKGROUND:Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5121-z
更新日期:2018-11-29 00:00:00
abstract:BACKGROUND:Identification of acute or recent hepatitis C virus (HCV) infections is important for detecting outbreaks and devising timely public health interventions for interruption of transmission. Epidemiological investigations and chemistry-based laboratory tests are 2 main approaches that are available for identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4269-2
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomic...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S1-S5
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ripening, including changes in fruit color and taste. However, research at the molecular level is l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-19
更新日期:2012-01-13 00:00:00
abstract:BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-632
更新日期:2010-11-15 00:00:00
abstract:BACKGROUND:Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits. RESULTS:Fruits of Coratina, a ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-399
更新日期:2009-08-26 00:00:00
abstract:BACKGROUND:Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-58
更新日期:2004-08-20 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in psoriasis are still incompletely understood. The objective of the present study was to characterize th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-825
更新日期:2013-11-23 00:00:00
abstract:BACKGROUND:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-388
更新日期:2009-08-21 00:00:00
abstract:BACKGROUND:The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing')...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-21
更新日期:2010-01-11 00:00:00