Abstract:
BACKGROUND:Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. RESULTS:We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. CONCLUSIONS:This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Shen Y,Wang L,Fu J,Xu X,Yue GH,Li Jdoi
10.1186/s12864-019-5872-1subject
Has Abstractpub_date
2019-06-07 00:00:00pages
467issue
1issn
1471-2164pii
10.1186/s12864-019-5872-1journal_volume
20pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by comparing their transcriptional responses between sleeping mice and those kept awake, sacrificed at ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07050-7
更新日期:2020-09-14 00:00:00
abstract:BACKGROUND:Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copie...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1860-2
更新日期:2015-09-03 00:00:00
abstract:BACKGROUND:The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-109
更新日期:2009-03-15 00:00:00
abstract:BACKGROUND:Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2047-6
更新日期:2015-11-05 00:00:00
abstract:BACKGROUND:Male and female vertebrates typically differ in a range of characteristics, from morphology to physiology to behavior, which are influenced by factors such as the social environment and the internal hormonal and genetic milieu. However, sex differences in gene expression profiles in the brains of vertebrates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-905
更新日期:2014-10-17 00:00:00
abstract:BACKGROUND:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic al...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-115
更新日期:2008-03-03 00:00:00
abstract:BACKGROUND:Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia L.) is a polyploid plant and a pioneer tree species due to its wide ranging adaptability to adver...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4038-2
更新日期:2017-08-22 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:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced chan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07164-y
更新日期:2020-11-04 00:00:00
abstract:BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1004
更新日期:2014-11-20 00:00:00
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:Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6342-5
更新日期:2019-12-05 00:00:00
abstract:BACKGROUND:The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essenti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1736-5
更新日期:2015-07-14 00:00:00
abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearra...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-561
更新日期:2014-07-04 00:00:00
abstract:BACKGROUND:Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5683-4
更新日期:2019-04-24 00:00:00
abstract:BACKGROUND:Dictyostelium discoideum is frequently subjected to environmental changes in its natural habitat, the forest soil. In order to survive, the organism had to develop effective mechanisms to sense and respond to such changes. When cells are faced with a hypertonic environment a complex response is triggered. It...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-123
更新日期:2007-05-21 00:00:00
abstract:BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-260
更新日期:2010-04-22 00:00:00
abstract:BACKGROUND:Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful markers for investigating population genetic structures, systematics and phylogenetics of organisms...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-224
更新日期:2008-05-16 00:00:00
abstract:BACKGROUND:The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-367
更新日期:2010-06-10 00:00:00
abstract:BACKGROUND:Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs) can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by the human genome project allows us to identify new GPRs by in silico homology screening, and to predi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-3-17
更新日期:2002-07-05 00:00:00
abstract:BACKGROUND:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1053
更新日期:2014-12-03 00:00:00
abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6244-6
更新日期:2019-11-14 00:00:00
abstract:BACKGROUND:Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. RESULTS:In the current work, we carried out a bioinformatics analysis of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-155
更新日期:2009-04-09 00:00:00
abstract:BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4079-6
更新日期:2017-08-31 00:00:00
abstract:BACKGROUND:Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS:Here,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4469-4
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-98
更新日期:2005-07-13 00:00:00
abstract:BACKGROUND:Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-214
更新日期:2007-07-04 00:00:00
abstract:BACKGROUND:The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-933
更新日期:2014-10-25 00:00:00
abstract:BACKGROUND:The androgen receptor plays a critical role throughout the progression of prostate cancer and is an important drug target for this disease. While chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) is becoming an essential tool for studying transcription and chromatin modifica...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-355
更新日期:2012-07-31 00:00:00
abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-34
更新日期:2007-01-29 00:00:00