Abstract:
:Stem blister canker, caused by Botryosphaeria dothidea, is becoming the most serious disease of poplar in China. The molecular basis of the poplar in response to stem blister canker is not well understood. To reveal the global transcriptional changes of poplar to infection by B. dothidea, Solexa paired-end sequencing of complementary DNAs (cDNAs) from control (NB) and pathogen-treated samples (WB) was performed, resulting in a total of 339,283 transcripts and 183,881 unigenes. A total of 206,586 transcripts were differentially expressed in response to pathogen stress (false discovery rate ≤0.05 and an absolute value of log2Ratio (NB/WB) ≥1). In enrichment analysis, energy metabolism and redox reaction-related macromolecules were accumulated significantly in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses, indicating components of dynamic defense against the fungus. A total of 852 transcripts (575 upregulated and 277 downregulated transcripts) potentially involved in plant-pathogen interaction were also differentially regulated, including genes encoding proteins linked to signal transduction (putative leucine-rich repeat (LRR) protein kinases and calcium-binding proteins), defense (pathogenesis-related protein 1), and cofactors (jasmonate-ZIM-domain-containing proteins and heat shock proteins). Moreover, transcripts encoding glutathione S-transferase (GST) were accumulated to high levels, revealing key genes and proteins potentially related to pathogen resistance. Poplar RNA sequence data were validated by quantitative real-time PCR (RT-qPCR), which revealed a highly reliability of the transcriptomic profiling data.
journal_name
Funct Integr Genomicsjournal_title
Functional & integrative genomicsauthors
Liao W,Ji L,Wang J,Chen Z,Ye M,Ma H,An Xdoi
10.1007/s10142-014-0379-ysubject
Has Abstractpub_date
2014-09-01 00:00:00pages
517-29issue
3eissn
1438-793Xissn
1438-7948journal_volume
14pub_type
杂志文章abstract::Tuber mustard (Brassica juncea (L.) Czern. et Coss. var. tumida Tsen et Lee) is an important vegetable crop with a characteristic of expanded stem that is edible. The underlying molecular mechanism of the stem expansion is not well understood. Here, we reported that a total of 51 differentially expressed fragments (DE...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0458-8
更新日期:2015-11-01 00:00:00
abstract::Late blight is a serious economic threat to potato crop, sometimes leading to complete crop loss. The resistance in potato to late blight can be qualitative or quantitative in nature. Qualitative resistance is not durable. Though quantitative resistance is durable, the breeding is challenging due to polygenic inherita...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-013-0358-8
更新日期:2014-06-01 00:00:00
abstract::The aim of this study was to examine the effect of abscisic acid (ABA), sucrose, and auxin on grape fruit development and to assess the mechanism of these three factors on the grape fruit ripening process. Different concentrations of ABA, sucrose, and auxin were used to treat the grape fruit, and the ripening-related ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-017-0546-z
更新日期:2017-07-01 00:00:00
abstract::The ATP-binding cassette (ABC) transporters are a large family of proteins responsible for the translocation of a variety of compounds across the membranes of both prokaryotes and eukaryotes. The inter-protein and intra-protein interactions in these traffic ATPases are still only poorly understood. In the present stud...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-001-0040-4
更新日期:2002-04-01 00:00:00
abstract::The ubiquitous cell membrane proteins called aquaporins are now firmly established as channel proteins that control the specific transport of water molecules across cell membranes in all living organisms. The aquaporins are thus likely to be of fundamental significance to all facets of plant growth and development aff...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-007-0049-4
更新日期:2007-10-01 00:00:00
abstract::EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs ((SSR)ESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl scrip...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-004-0128-8
更新日期:2005-04-01 00:00:00
abstract::Aminopeptidase H11, an integral membrane glycoprotein present only in the gut of Haemonchus contortus, could provide substantial protection as shown by 90% reduction in fecal egg counts, while its recombinant version expressed in E. coli induced little. To investigate the characteristics further, we amplified mRNA of ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-010-0172-5
更新日期:2010-11-01 00:00:00
abstract::The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consume...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-019-00684-1
更新日期:2019-09-01 00:00:00
abstract::Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-012-0274-3
更新日期:2012-06-01 00:00:00
abstract::The response of a grass halophyte Spartina alterniflora at early stages of salt stress was investigated through generation and systematic analysis of expressed sequence tags (ESTs) from both leaf and root tissues. Random EST sequencing produced 1,227 quality ESTs, which were clustered into 127 contigs, and 368 were si...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-008-0075-x
更新日期:2008-08-01 00:00:00
abstract::Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multi...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-016-0530-z
更新日期:2017-01-01 00:00:00
abstract::As the amino acid storing organelle, the protein bodies provide nutrients for embryo development, seed germination and early seedling growth through storage proteolysis in cereal plants, such as wheat and rice. In protein bodies, the monomeric and polymeric prolamins, i.e. gliadins and glutenins, form gluten and play ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-010-0196-x
更新日期:2011-03-01 00:00:00
abstract::The symbiotic N(2)-fixing alpha-proteobacterium Sinorhizobium meliloti has three replicons: a circular chromosome (3.7 Mb) and two smaller replicons, pSymA (1.4 Mb) and pSymB (1.7 Mb). Sequence analysis has revealed that an essential gene is carried on pSymB, which brings into question whether pSymB should be consider...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-002-0068-0
更新日期:2002-11-01 00:00:00
abstract::Rhizoctonia solani AG1-IA is a soil-borne necrotrophic pathogen that causes devastating rice sheath blight disease in rice-growing regions worldwide. Sclerotia play an important role in the life cycle of R. solani AG1-IA. In this study, RNA sequencing was used to investigate the transcriptomic dynamics of sclerotial d...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-019-00677-0
更新日期:2019-09-01 00:00:00
abstract::The IbeA (ibe10) gene is an invasion determinant contributing to E. coli K1 invasion of the blood-brain barrier. This gene has been cloned and characterized from the chromosome of an invasive cerebrospinal fluid isolate of E. coli K1, strain RS218 (018:K1: H7). In the present study, a genetic island of meningitic E. c...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s101420100039
更新日期:2001-09-01 00:00:00
abstract::Microarray experiments are being increasingly used in molecular biology. A common task is to detect genes with differential expression across two experimental conditions, such as two different tissues or the same tissue at two time points of biological development. To take proper account of statistical variability, so...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-002-0066-2
更新日期:2002-08-01 00:00:00
abstract::Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In thi...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0437-0
更新日期:2015-07-01 00:00:00
abstract::Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alig...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-009-0129-8
更新日期:2009-11-01 00:00:00
abstract::Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-012-0293-0
更新日期:2012-08-01 00:00:00
abstract::MicroRNAs (miRNAs) are small RNAs (sRNAs) that regulate gene expression in development and adaptive responses to the environment. The early days in the sRNA field was one of the most exciting and promising moments in modern biology, attracting large investments to the understanding of the underlining mechanisms and th...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-016-0513-0
更新日期:2017-05-01 00:00:00
abstract::Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conserv...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-013-0319-2
更新日期:2013-03-01 00:00:00
abstract::Fungal species are potential dye decomposers since these secrete spectra of extracellular enzymes involved in catabolism. However, cellular mechanisms underlying azo dye catalysis and detoxification are incompletely understood and obscure. A potential strain designated as Penicillium oxalicum SAR-3 demonstrated broad-...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-014-0405-0
更新日期:2014-12-01 00:00:00
abstract::Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes s...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-020-00735-y
更新日期:2020-07-01 00:00:00
abstract::In theory, gene therapy is a simple concept which holds great promise as a cure for disease. In practice, however, considerable obstacles have to be overcome, including problems with safe and efficient gene delivery and stable gene expression. This review gives an overview on the history of gene therapy and analyses s...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s101420000011
更新日期:2000-09-01 00:00:00
abstract::The root-knot nematode Meloidogyne incognita is among the most damaging plant-parasitic pests of several crops including cotton (Gossypium hirsutum) and tomato (Lycopersicon escultentum). Recently, a genome has become available for M. incognita, which greatly facilitates investigation of the interactions between M. in...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0472-x
更新日期:2016-03-01 00:00:00
abstract::Medicago sativa L. (alfalfa) 'Zhaodong' is an important forage legume that can safely survive in northern China where winter temperatures reach as low as -30 °C. Survival of alfalfa following freezing stress depends on the amount and revival ability of crown buds. In order to investigate the molecular mechanisms of fr...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-016-0500-5
更新日期:2016-09-01 00:00:00
abstract::Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-007-0052-9
更新日期:2008-02-01 00:00:00
abstract::In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergenc...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-018-0605-0
更新日期:2018-07-01 00:00:00
abstract::The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC librar...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-011-0237-0
更新日期:2011-12-01 00:00:00
abstract::Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-011-0250-3
更新日期:2012-03-01 00:00:00