Abstract:
BACKGROUND:Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. METHODS:We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). RESULTS:Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. CONCLUSIONS:The present analyses of the visceral fat transcriptome in chickens divergently selected for a large difference in growth rate and abdominal fatness clearly demonstrate that abdominal fat is a very dynamic metabolic and endocrine organ in the chicken. The HG chickens overexpress many transcription factors and their direct target genes, which should enhance in situ lipogenesis and ultimately adiposity. Our observation of enhanced expression of hemostasis and endocrine-signaling genes in diminished abdominal fat of LG cockerels provides insight into genetic mechanisms involved in divergence of abdominal fatness and somatic growth in avian and perhaps mammalian species, including humans.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Resnyk CW,Carré W,Wang X,Porter TE,Simon J,Le Bihan-Duval E,Duclos MJ,Aggrey SE,Cogburn LAdoi
10.1186/s12864-017-4035-5subject
Has Abstractpub_date
2017-08-16 00:00:00pages
626issue
1issn
1471-2164pii
10.1186/s12864-017-4035-5journal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently. RESULTS:This work focuses on providing a tool for dis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6610-4
更新日期:2020-04-16 00:00:00
abstract:BACKGROUND:Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted specul...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3626-5
更新日期:2017-03-31 00:00:00
abstract:BACKGROUND:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1658-2
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4012-z
更新日期:2017-08-08 00:00:00
abstract:BACKGROUND:To date, oil-rich plants are the main source of biodiesel products. Because concerns have been voiced about the impact of oil-crop cultivation on the price of food commodities, the interest in oil plants not used for food production and amenable to cultivation on non-agricultural land has soared. As a non-fo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-462
更新日期:2010-08-06 00:00:00
abstract:BACKGROUND:Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-986
更新日期:2014-11-18 00:00:00
abstract:BACKGROUND:Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koala...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-667
更新日期:2014-08-08 00:00:00
abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2139-3
更新日期:2015-11-14 00:00:00
abstract:BACKGROUND:The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an ep...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4052-4
更新日期:2017-08-23 00:00:00
abstract:BACKGROUND:Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. RESULTS:In this study, 48 CIPK genes (SsCIPKs) were identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07264-9
更新日期:2020-12-07 00:00:00
abstract:BACKGROUND:Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07027-6
更新日期:2020-10-15 00:00:00
abstract:BACKGROUND:Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07108-6
更新日期:2020-10-17 00:00:00
abstract:BACKGROUND:Selenium (Se) is a trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine (SeU). Selenophosphate synthetase (SelD) is required for both utilization traits. However, previous research also revealed SelDs in two organisms lacking Sec and SeU, suggest...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-251
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4394-y
更新日期:2018-01-06 00:00:00
abstract:BACKGROUND:Most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. Inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. Animal serpins exert...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-449
更新日期:2012-09-04 00:00:00
abstract:BACKGROUND:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-281
更新日期:2012-06-24 00:00:00
abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-188
更新日期:2012-05-15 00:00:00
abstract:BACKGROUND:A fundamental requirement for genomic studies is the availability of genetic material of good quality and quantity. The desired quantity and quality are often hard to obtain when target DNA is composed of complex mixtures of relatively short DNA fragments. Here, we sought to develop a method to representativ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-415
更新日期:2008-09-15 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, mos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5497-4
更新日期:2019-02-15 00:00:00
abstract:BACKGROUND:The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expressio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3584-y
更新日期:2017-02-23 00:00:00
abstract:BACKGROUND:Sand fly saliva plays an important role in blood feeding and Leishmania transmission as it was shown to increase parasite virulence. On the other hand, immunity to salivary components impedes the establishment of infection. Therefore, it is most desirable to gain a deeper insight into the composition of sali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-282
更新日期:2009-06-25 00:00:00
abstract:BACKGROUND:Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4320-3
更新日期:2017-12-15 00:00:00
abstract:BACKGROUND:Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07113-9
更新日期:2020-10-21 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:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6391-9
更新日期:2019-12-26 00:00:00
abstract:BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3731-5
更新日期:2017-05-24 00:00:00
abstract:BACKGROUND:It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-587
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-564
更新日期:2012-10-22 00:00:00
abstract:BACKGROUND:An important subfamily of membrane proteins are the transmembrane alpha-helical proteins, in which the membrane-spanning regions are made up of alpha-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmem...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S1-S7
更新日期:2008-01-01 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