Abstract:
BACKGROUND:Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available. RESULTS:We examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles, and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast, and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent association with gene density. CONCLUSION:Our results indicate global repeat content variation in the heterotic populations of maize has not diverged, and is uncoupled from population stratification at SNP loci. We show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Renny-Byfield S,Baumgarten Adoi
10.1186/s12864-020-6517-0subject
Has Abstractpub_date
2020-01-30 00:00:00pages
98issue
1issn
1471-2164pii
10.1186/s12864-020-6517-0journal_volume
21pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2176-y
更新日期:2015-11-10 00:00:00
abstract:BACKGROUND:Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-60
更新日期:2012-02-06 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short non-coding RNAs that are emerging as important post-transcriptional regulators of neuronal and synaptic development. The precise impact of miRNAs on presynaptic function and neurotransmission remains, however, poorly understood. RESULTS:Here, we identify miR-27b-an abundant neur...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3139-7
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S7-S3
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Emerging evidence has been experimentally confirmed the tissue-specific expression of circRNAs (circRNAs). Global identification of human tissue-specific circRNAs is crucial for the functionality study, which facilitates the discovery of circRNAs for potential diagnostic biomarkers. RESULTS:In this study, c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4335-9
更新日期:2018-01-19 00:00:00
abstract:BACKGROUND:Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1752-5
更新日期:2015-07-16 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:The question of whether synonymous codon choice is affected by cellular tRNA abundance has been positively answered in many organisms. In some recent works, concerning the human genome, this relation has been studied, but no conclusive answers have been found. In the human genome, the variation in base compo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-67
更新日期:2006-04-03 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: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:Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4565-5
更新日期:2018-03-12 00:00:00
abstract:BACKGROUND:Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. RES...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-578
更新日期:2008-12-02 00:00:00
abstract:BACKGROUND:Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In area...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-719
更新日期:2014-08-26 00:00:00
abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-680
更新日期:2010-11-30 00:00:00
abstract:BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-463
更新日期:2008-10-08 00:00:00
abstract:BACKGROUND:Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still un...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3403-x
更新日期:2017-01-05 00:00:00
abstract:BACKGROUND:Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity make the promoter attractive for in silico analysis and reporter gene studies in zebrafish (Danio re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-3-25
更新日期:2002-08-21 00:00:00
abstract:BACKGROUND:Drosophila melanogaster females show changes in behavior and physiology after mating that are thought to maximize the number of progeny resulting from the most recent copulation. Sperm and seminal fluid proteins induce post-mating changes in females, however, very little is known about the resulting gene exp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-541
更新日期:2010-10-06 00:00:00
abstract:BACKGROUND:Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6322-9
更新日期:2019-12-03 00:00:00
abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-630
更新日期:2014-07-28 00:00:00
abstract:BACKGROUND:It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-154
更新日期:2005-11-04 00:00:00
abstract:BACKGROUND:Cotton, one of the world's leading crops, is important to the world's textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-208
更新日期:2013-03-28 00:00:00
abstract:BACKGROUND:Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. RESULTS:Comparative analysis showed that the structure and evolutionary patterns of the I...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-743
更新日期:2014-08-30 00:00:00
abstract:BACKGROUND:Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-103
更新日期:2008-02-27 00:00:00
abstract:BACKGROUND:During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of genes in a genome. Our aim is to compute the evolutionary distance b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6611-3
更新日期:2020-04-16 00:00:00
abstract:BACKGROUND:As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Mandarin fish accept only live prey fish and refuse dead p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-601
更新日期:2013-09-05 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:Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-289
更新日期:2011-06-03 00:00:00
abstract:BACKGROUND:The purpose of this research was to develop a novel information theoretic method and an efficient algorithm for analyzing the gene-gene (GGI) and gene-environmental interactions (GEI) associated with quantitative traits (QT). The method is built on two information-theoretic metrics, the k-way interaction inf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-509
更新日期:2009-11-04 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00