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 replication in chloroplasts. RESULTS:We address this issue in our current study by analyzing nucleotide composition in genome regions between known replication origins, with an aim to reveal any adenine to guanine deamination gradients. These gradual linear gradients typically result from the accumulation of deaminations over the time spent single-stranded by one of the strands of the circular molecule during replication and can, therefore, be used to model the course of replication. Our linear regression analyses on the nucleotide compositions of the non-coding regions and the synonymous third codon position of coding regions, between pairs of replication origins, reveal the existence of significant adenine to guanine deamination gradients in portions overlapping the Small Single Copy (SSC) and the Large Single Copy (LSC) regions between inverted repeats. These gradients increase bi-directionally from the center of each region towards the respective ends, suggesting that both the strands were left single-stranded during replication. CONCLUSION:Single-stranded regions of the genome and gradients in time that these regions are left single-stranded, as revealed by our nucleotide composition analyses, appear to converge with the original bi-directional dual displacement loop model and restore evidence for its existence as the primary mechanism. Other proposed faster modes such as homologous recombination and rolling circle initiation could exist in addition to this primary mechanism to facilitate homoplasmy among the intra-cellular chloroplast population.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Krishnan NM,Rao BJdoi
10.1186/1471-2164-10-237subject
Has Abstractpub_date
2009-05-20 00:00:00pages
237issn
1471-2164pii
1471-2164-10-237journal_volume
10pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high inciden...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-379
更新日期:2009-08-17 00:00:00
abstract:BACKGROUND:Grass carp (Ctenopharyngodon idella) belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards under...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-135
更新日期:2010-02-24 00:00:00
abstract:BACKGROUND:Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi, but it rapidly and proficiently kills Brugia malayi microfilariae by melanotic encapsulation. Because B. malayi and B. pahangi are morphologically and biologically similar, the Armigeres-Brugia system serves as a valuable model for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-463
更新日期:2007-12-18 00:00:00
abstract:BACKGROUND:The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-888
更新日期:2013-12-17 00:00:00
abstract:BACKGROUND:Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-17
更新日期:2009-01-12 00:00:00
abstract:BACKGROUND:Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported. RESULTS:The present study identified 134 GmPP2C...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06877-4
更新日期:2020-07-06 00:00:00
abstract:BACKGROUND:Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of severa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1711-1
更新日期:2015-07-31 00:00:00
abstract:BACKGROUND:The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2124-x
更新日期:2015-12-07 00:00:00
abstract:BACKGROUND:Several global transcriptomic and proteomic approaches have been applied in order to obtain new molecular insights on skeletal myogenesis, but none has generated any specific data on glycogenome expression, and thus on the role of glycan structures in this process, despite the involvement of glycoconjugates ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-483
更新日期:2009-10-20 00:00:00
abstract:BACKGROUND:Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic archit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4837-0
更新日期:2018-06-13 00:00:00
abstract:BACKGROUND:Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4567-3
更新日期:2018-03-02 00:00:00
abstract:BACKGROUND:The programmed cell death 2 (Pdcd2) gene on mouse chromosome 17 was evaluated as a member of a highly conserved synteny, a candidate for an imprinted locus, and a candidate for the Hybrid sterility 1 (Hst1) gene. RESULTS:New mouse transcripts were identified at this locus: an alternative Pdcd2 mRNA skipping...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-20
更新日期:2007-01-18 00:00:00
abstract:BACKGROUND:Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-262
更新日期:2012-06-21 00:00:00
abstract:BACKGROUND:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1376-9
更新日期:2015-03-25 00:00:00
abstract:BACKGROUND:Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candid...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-624
更新日期:2013-09-16 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:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06888-1
更新日期:2020-09-23 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression implicated in multiple cellular processes. Cyclic stretch of alveoli is characteristic of mechanical ventilation, and is postulated to be partly responsible for the lung injury and inflammation in ventilator-induced lung injury. We pro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-154
更新日期:2012-04-26 00:00:00
abstract:BACKGROUND:Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large per...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-156
更新日期:2014-02-24 00:00:00
abstract:BACKGROUND:Host-specific environmental factors induce changes in Bacillus anthracis gene transcription during infection. A global transcription regulator, CodY, plays a pivotal role in regulating central metabolism, biosynthesis, and virulence in B. anthracis. In this study, we utilized RNA-sequencing to assess changes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3004-8
更新日期:2016-08-17 00:00:00
abstract:BACKGROUND:The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4788-5
更新日期:2018-05-25 00:00:00
abstract:BACKGROUND:The contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early onset. The current protocols of continuous clinical follow-up of relatives of such patients are costl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S1-S3
更新日期:2015-01-01 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:Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabolites employed as defense-related phytoalexins. To unravel the fungal adaptive mechanisms to vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4739-1
更新日期:2018-05-10 00:00:00
abstract:BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S3-S14
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:Inferring the microbial interaction networks (MINs) and modeling their dynamics are critical in understanding the mechanisms of the bacterial ecosystem and designing antibiotic and/or probiotic therapies. Recently, several approaches were proposed to infer MINs using the generalized Lotka-Volterra (gLV) mode...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3605-x
更新日期:2017-03-27 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:Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of sm...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-40
更新日期:2003-09-30 00:00:00
abstract:BACKGROUND:Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive development and to elucidate the dynamic regulation of the transcriptomic response during the early-juv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5232-6
更新日期:2018-11-19 00:00:00
abstract:BACKGROUND:Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. I...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1272-3
更新日期:2015-02-25 00:00:00