Abstract:
BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general. RESULTS:By embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates' epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms. CONCLUSIONS:Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Xiang H,Li X,Dai F,Xu X,Tan A,Chen L,Zhang G,Ding Y,Li Q,Lian J,Willden A,Guo Q,Xia Q,Wang J,Wang Wdoi
10.1186/1471-2164-14-646subject
Has Abstractpub_date
2013-09-23 00:00:00pages
646issn
1471-2164pii
1471-2164-14-646journal_volume
14pub_type
杂志文章相关文献
BMC GENOMICS文献大全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:Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1259-0
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-392
更新日期:2011-08-03 00:00:00
abstract:BACKGROUND:In most species of mammals, the TRB locus has the common feature of a library of TRBV genes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a single TRBD gene, 6-7 TRBJ genes and one TRBC gene. An enhancer located at the 3'end of the last TRBC and a well-defined promo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-3
更新日期:2010-01-04 00:00:00
abstract:BACKGROUND:The trypanosomatids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi cause some of the most debilitating diseases of humankind: cutaneous leishmaniasis, African sleeping sickness, and Chagas disease. These protozoa possess complex life cycles that involve development in mammalian and insect hosts, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-127
更新日期:2005-09-15 00:00:00
abstract:BACKGROUND:Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus), is an acquired pathogen and the primary cause of nosocomial infections worldwide. In S. aureus, teichoic acid is an essential component of the cell wall, and its biosynthesis is not yet well characterized. Studies in Bacillus subtilis have disc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-74
更新日期:2006-04-05 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:Many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. Mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. Such a pattern could also arise from selection coupled ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-369
更新日期:2007-10-12 00:00:00
abstract:BACKGROUND:Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age gro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1470-z
更新日期:2015-04-08 00:00:00
abstract:BACKGROUND:Pharmacological and gene ablation studies have demonstrated the crucial role of the endocrine function of the heart as mediated by the polypeptide hormones ANF and BNP in the maintenance of cardiovascular homeostasis. The importance of these studies lies on the fact that hypertension and chronic congestive h...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-254
更新日期:2009-06-01 00:00:00
abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-241
更新日期:2009-05-22 00:00:00
abstract:BACKGROUND:Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S8-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that chang...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4519-y
更新日期:2018-02-22 00:00:00
abstract:BACKGROUND:Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. RESULTS:In this study, we constructed a high-density genetic map of the P...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07254-x
更新日期:2020-12-02 00:00:00
abstract:BACKGROUND:The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to att...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1939-9
更新日期:2015-10-09 00:00:00
abstract:MOTIVATION:With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S6-S7
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1472-x
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-637
更新日期:2008-12-31 00:00:00
abstract:BACKGROUND:Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds of a rolling circle mechanism. This standard model is being challenged by the recent proposition of homologous recombination-mediated rep...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-237
更新日期:2009-05-20 00:00:00
abstract:BACKGROUND:Chromosome 17q21.31 contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry. Two divergent MAPT haplotypes, H1 and H2 are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. The MAPT H1 haploty...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-458
更新日期:2012-09-06 00:00:00
abstract:BACKGROUND:Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3146-8
更新日期:2016-10-12 00:00:00
abstract:BACKGROUND:Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-571
更新日期:2010-10-16 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:Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-398
更新日期:2010-06-23 00:00:00
abstract:BACKGROUND:The mosquito Anopheles gambiae is a major vector of human malaria. Increasing evidence indicates that blood cells (hemocytes) comprise an essential arm of the mosquito innate immune response against both bacteria and malaria parasites. To further characterize the role of hemocytes in mosquito immunity, we un...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-257
更新日期:2009-06-05 00:00:00
abstract:BACKGROUND:Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different droug...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4321-2
更新日期:2017-12-15 00:00:00
abstract:BACKGROUND:Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein components of non-coding ribonucleoprotein (ncRNP) particles by RNA interference (RNAi) may therefore aff...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-278
更新日期:2008-06-11 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:microRNA (miRNA) expression plays an influential role in cancer classification and malignancy, and miRNAs are feasible as alternative diagnostic markers for pancreatic cancer, a highly aggressive neoplasm with silent early symptoms, high metastatic potential, and resistance to conventional therapies. METHOD...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S9-S4
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:gammadelta T cells differ from alphabeta T cells with regard to the types of antigen with which their T cell receptors interact; gammadelta T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are considered a "gammadelta T cell high" species indicating they have an increased pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-100
更新日期:2010-02-09 00:00:00