Abstract:
BACKGROUND:Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency. Herein, we identified PAP homologs in the genomes of 10 vegetable species, along with Arabidopsis thaliana and Amborella trichopoda as references, to provide fundamental knowledge for this family. RESULTS:Phylogenetic analysis of protein sequences revealed nine distinct clades, indicating that functional differentiation of extant PAPs was established prior to the emergence of early angiosperms, and conserved among homologs in each clade. Analysis of transcript abundance in different tissues (root, stem, leaf, flower, and fruit) and following phosphates (Pi) starvation treatments from published RNA-seq transcriptome datasets facilitated comprehensive evaluation of expression patterns, and some groups of tissue-specific and Pi starvation-induced PAPs were characterised. Conserved motifs identified from upstream sequences of homologs that are highly expressed in particular tissues or following starvation treatment suggests that divergence in PAP gene expression is associated with cis-acting elements in promoters. CONCLUSIONS:The genome-wide analysis of PAP enzyme structure and transcriptional expression patterns advance our understanding of PAP family in vegetables genomes. Therefore, PAP homologs with known enzyme structures and expression profiles could serve as targets for plant breeding and/or genetic engineering programs to improve P acquisition and use.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Xie L,Shang Qdoi
10.1186/s12864-018-5022-1subject
Has Abstractpub_date
2018-08-31 00:00:00pages
646issue
1issn
1471-2164pii
10.1186/s12864-018-5022-1journal_volume
19pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3782-7
更新日期:2017-05-22 00:00:00
abstract:BACKGROUND:We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS:The assembly process consisted of multipl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-180
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1020
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1154
更新日期:2014-12-20 00:00:00
abstract:BACKGROUND:Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. RESULTS:We describe a Web-...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S5-S13
更新日期:2013-01-01 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:Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-134
更新日期:2006-06-01 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: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:Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5-245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only rec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2195-8
更新日期:2015-11-14 00:00:00
abstract:BACKGROUND:Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2471-2
更新日期:2016-02-25 00:00:00
abstract:BACKGROUND:Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in young children. The degree of disease severity is determined by the host response to infection. Lung macrophages play an important early role in the host response to infection and we have used a systems-based appr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-190
更新日期:2013-03-18 00:00:00
abstract:BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-150
更新日期:2010-03-04 00:00:00
abstract:BACKGROUND:The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing')...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-21
更新日期:2010-01-11 00:00:00
abstract:BACKGROUND:The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, wh...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S3-S13
更新日期:2010-12-01 00:00:00
abstract:BACKGROUND:Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. A...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-325
更新日期:2012-07-20 00:00:00
abstract:BACKGROUND:With the development of several new technologies using synthetic biology, it is possible to engineer genetically intractable organisms including Mycoplasma mycoides subspecies capri (Mmc), by cloning the intact bacterial genome in yeast, using the host yeast's genetic tools to modify the cloned genome, and s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1180
更新日期:2014-12-24 00:00:00
abstract:BACKGROUND:Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1031
更新日期:2014-11-27 00:00:00
abstract:BACKGROUND:The sequencing of the cow genome was recently published (Btau_4.0 assembly). A second, alternate cow genome assembly (UMD2), based on the same raw sequence data, was also published. The two assemblies have been subsequently updated to Btau_4.2 and UMD3.1, respectively. RESULTS:We compared the Btau_4.2 and U...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-639
更新日期:2011-12-30 00:00:00
abstract:BACKGROUND:Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07334-y
更新日期:2021-01-08 00:00:00
abstract:BACKGROUND:The eyes and skin are obvious retinoid target organs. Vitamin A deficiency causes night blindness and retinoids are widely used to treat acne and psoriasis. However, more than 90% of total body retinol is stored in liver stellate cells. In addition, hepatocytes produce the largest amount of retinol binding p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-575
更新日期:2013-08-28 00:00:00
abstract:BACKGROUND:Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference to compare signal intensities to reliably determine presence or divergence each DNA fragment. Howeve...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-522
更新日期:2009-11-13 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-291
更新日期:2011-06-04 00:00:00
abstract:BACKGROUND:One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S5-S4
更新日期:2011-12-23 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:Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5379-1
更新日期:2019-01-03 00:00:00
abstract:BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6552-x
更新日期:2020-02-11 00:00:00
abstract:BACKGROUND:Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6297-6
更新日期:2019-12-24 00:00:00
abstract:BACKGROUND:Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1074
更新日期:2014-12-06 00:00:00
abstract:BACKGROUND:The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative ana...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4714-x
更新日期:2018-05-09 00:00:00