Abstract:
BACKGROUND:Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton's content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limit secondary production in the major zooplankton herbivore genus Daphnia. Despite extensive research efforts on the biological model organism Daphnia, and the availability of several Daphnia genomes, little is known regarding the molecular mechanisms underlying the limitations in Daphnia related to dietary EPA availability. RESULTS:We used RNA-seq to analyse the transcriptomic response of Daphnia magna which were fed with two different diets - each with or without supplementation of EPA - at two different temperature levels (15 and 20 °C). The transcripts were mapped to the D. magna genome assembly version 2.4, containing 26,646 translations. When D. magna fed on green alga, changing the temperature provoked a differential expression of 2001 transcripts, and in cyanobacteria-fed daphnia, 3385 transcripts were affected. The supplementation of EPA affected 1635 (on the green algal diet), or 175 transcripts (on the cyanobacterial diet), respectively. Combined effects for diet and temperature were also observed (669 for the green algal and 128 transcripts for the cyanobacterial diet). Searching for orthologous genes (COG-analysis) yielded a functional overview of the altered transcriptomes. Cross-matched transcript sets from both feed types were compiled to illuminate core responses to the factors temperature and EPA-supplementation. CONCLUSIONS:Our highly controlled eco-physiological experiments revealed an orchestrated response of genes involved in the transformation and signalling of essential fatty acids, including eicosanoid-signalling pathways with potential immune functions. We provide an overview of downstream-regulated genes, which contribute to enhance growth and reproductive output. We also identified numerous EPA-responsive candidate genes of yet unknown function, which constitute new targets for future studies on the molecular basis of EPA-dependent effects at the freshwater plant-herbivore interface.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Windisch HS,Fink Pdoi
10.1186/s12864-019-6268-ysubject
Has Abstractpub_date
2019-11-21 00:00:00pages
894issue
1issn
1471-2164pii
10.1186/s12864-019-6268-yjournal_volume
20pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Recent research has revealed that polymorphic behavioral strategies shape intra-and interspecific interactions and contribute to fitness in many animal species. A better understanding of the proximate mechanisms underlying these behavioral syndromes will enhance our grasp this phenomenon. Spiders in the genu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6172-5
更新日期:2019-11-22 00:00:00
abstract:BACKGROUND:An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2965-y
更新日期:2016-08-15 00:00:00
abstract:BACKGROUND:Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast' variation pattern of poplar at the single-base level during...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4813-8
更新日期:2018-05-29 00:00:00
abstract:BACKGROUND:The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-212
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epig...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4814-7
更新日期:2018-06-04 00:00:00
abstract:BACKGROUND:Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06917-z
更新日期:2020-07-22 00:00:00
abstract:BACKGROUND:Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07177-7
更新日期:2020-11-09 00:00:00
abstract:BACKGROUND:Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4606-0
更新日期:2018-04-06 00:00:00
abstract:BACKGROUND:Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3289-7
更新日期:2016-11-22 00:00:00
abstract:BACKGROUND:Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fru...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-552
更新日期:2013-08-14 00:00:00
abstract:BACKGROUND:Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and delaying the maturation of the B. cenocepacia-containing phagosome. We hypothesize that B. cenoce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-63
更新日期:2012-02-09 00:00:00
abstract:BACKGROUND:Crustacean moulting is a complex process involving many regulatory pathways. A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for Portunus pelag...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-147
更新日期:2011-03-12 00:00:00
abstract:BACKGROUND:Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutrit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-522
更新日期:2011-10-23 00:00:00
abstract:BACKGROUND:Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes, proteins, and reactions (GPRs). However, current gene-to-reaction formulation lacks the stoichiome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5979-4
更新日期:2019-08-15 00:00:00
abstract:BACKGROUND:In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-482
更新日期:2014-06-18 00:00:00
abstract:BACKGROUND:Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on singl...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-12-225
更新日期:2011-05-11 00:00:00
abstract:BACKGROUND:Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). RESULTS:We analyzed the postnatal transformation of adipose in sheep with a time course study of the ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1405-8
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. METHODS:In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5785-z
更新日期:2019-05-17 00:00:00
abstract:BACKGROUND:Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and he...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2928-3
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5092-0
更新日期:2018-10-01 00:00:00
abstract:BACKGROUND:Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowaday...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07346-8
更新日期:2021-01-07 00:00:00
abstract:BACKGROUND:The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. However, screening and retrieving appropriate candidates as well as handling false positives presents...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S4-S26
更新日期:2010-12-02 00:00:00
abstract:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6619-8
更新日期:2020-03-04 00:00:00
abstract:BACKGROUND:Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and functio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06942-y
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2690-6
更新日期:2016-05-18 00:00:00
abstract:BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-948
更新日期:2014-11-01 00:00:00
abstract:BACKGROUND:Genome-wide association studies show that most human traits and diseases are caused by a combination of environmental and genetic causes, with each one of these having a relatively small effect. In contrast, most therapies based on macromolecules like antibodies, antisense oligonucleotides or peptides focus ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1727-6
更新日期:2015-07-18 00:00:00
abstract:BACKGROUND:Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e.,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S13-S5
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. RESULTS:Here we report the finalized genome sequence of the envir...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4301-6
更新日期:2018-01-05 00:00:00
abstract:BACKGROUND:Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1769-9
更新日期:2015-07-22 00:00:00