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, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
journal_name
Funct Integr Genomicsjournal_title
Functional & integrative genomicsauthors
Appels R,Barrero R,Bellgard Mdoi
10.1007/s10142-013-0319-2subject
Has Abstractpub_date
2013-03-01 00:00:00pages
1-9issue
1eissn
1438-793Xissn
1438-7948journal_volume
13pub_type
杂志文章,评审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：:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes. In this study, we performed a large-scale analysis o...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-011-0252-1
更新日期：2012-03-01 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：:Comparative genomic analysis is the cornerstone of in silico-based approaches to understanding biological systems and processes across cereal species, such as rice, wheat and barley, in order to identify genes of agronomic interest. The size of the genomic repositories is nearly doubling every year, and this has signi...
journal_title：Functional & integrative genomics
pub_type： 杂志文章,评审
doi：10.1007/s10142-004-0102-5
更新日期：2004-03-01 00:00:00
abstract：:A cDNA library containing approximately 5,000 clones from germinating barley embryos was constructed and used to examine the variation in gene expression patterns during the first 4 days postimbibition. The expression profiles of embryos (including scutellum) from 4 to 96 h postimbibition were compared to a reference ...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-005-0133-6
更新日期：2005-07-01 00:00:00
abstract：:Aldo/keto reductases (AKRs) constitute a multitasking protein family that catalyzes diverse metabolic transformations including detoxification of stress generated reactive aldehydes. Yet this important protein family is poorly understood particularly in cyanobacteria, the ecologically most diverse and significant grou...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-017-0547-y
更新日期：2017-07-01 00:00:00
abstract：:The photosynthetic organs of the barley spike (lemma, palea, and awn) are considered resistant to drought. However, there is little information about gene expression in the spike organs under drought conditions. We compared response of the transcriptome of the lemma, palea, awn, and seed to drought stress using the Ba...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-009-0149-4
更新日期：2010-05-01 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：: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：: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：:Water temperature affects the survival, growth, immunity, reproduction, and productivity of farmed fish. The temperature beyond suitable range will disrupt the normal physiological activity. Common carp (Cyprinus carpio L.) is a representative eurythermic fish; they are able to sense and respond to changes in water te...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-018-0643-7
更新日期：2019-03-01 00:00:00
abstract：:Although the economic value of wheat flour is determined by the complement of gluten proteins, these proteins have been challenging to study because of the complexity of the major protein groups and the tremendous sequence diversity among wheat cultivars. The completion of a high-quality wheat genome sequence from the...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-019-00694-z
更新日期：2020-01-01 00:00:00
abstract：:MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-015-0453-0
更新日期：2015-09-01 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：: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：:Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but ...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-017-0586-4
更新日期：2018-03-01 00:00:00
abstract：:The expression of many genes encoding transcriptional activators in prokaryotes and eukaryotes is upregulated through positive feedback activation. During positive feedback activation, a transcriptional activator binds to its own promoter and thus increases its own expression as well as the expression of its target ge...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s101420000001
更新日期：2000-05-01 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：:Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene l...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-013-0327-2
更新日期：2013-08-01 00:00:00
abstract：:Barley (Hordeum vulgare L.) is one of the most important large-genome cereals with extensive genetic resources available in the public sector. Studies of genome organization in barley have been limited primarily to genetic markers and sparse sequence data. Here we report sequence analysis of 417.5 kb DNA from four BAC...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-002-0055-5
更新日期：2002-05-01 00:00:00
abstract：:GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress respo...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-018-0620-1
更新日期：2018-11-01 00:00:00
abstract：:Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold-acclimation-specific processes and pathways, we utilized cold acclimation tran...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-012-0303-2
更新日期：2013-03-01 00:00:00
abstract：:The whole genome expression pattern of Arabidopsis in response to the auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) was evaluated using the Affymetrix ATH1-121501 array. Arabidopsis plants were grown in vitro and were exposed to 1 mM 2,4-D for 1 h, after which time gene transcription levels were measured. I...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-004-0119-9
更新日期：2005-01-01 00:00:00
abstract：:GRAS domain genes are a group of important plant-specific transcription factors that have been reported to be involved in plant development. In order to know the roles of GRAS genes in grapevine, a widely cultivated fruit crop, the study on grapevine GRAS (VvGRAS) was carried out, and from which, 43 were identified fr...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-016-0479-y
更新日期：2016-07-01 00:00:00
abstract：:The oomycete pathogen Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is the causing agent of the destructive downy mildew disease in grapevine. Despite the advances towards elucidation of grapevine resistance mechanisms to downy mildew, increased knowledge of the biological and genetic components of the pathosy...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-012-0261-8
更新日期：2012-06-01 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：:Gastrointestinal nematodes of the genus Cooperia are arguably the most important parasites of cattle. The bovine jejunal transcriptome was characterized in response to Cooperia oncophora infection using RNA-seq technology. Approximately 71% of the 25,670 bovine genes were detected in the jejunal transcriptome. However...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-011-0259-7
更新日期：2012-03-01 00:00:00
abstract：:In the past decade, there has been an intense effort to comprehensively catalogue the expressed genes in the yeast Saccharomyces cerevisiae and to determine the absolute and relative abundance of transcript and protein levels under different cellular conditions. Several methods have been developed to monitor gene expr...
journal_title：Functional & integrative genomics
pub_type： 杂志文章,评审
doi：10.1007/s10142-002-0065-3
更新日期：2002-09-01 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：:Natural selection drives species adaptations to biotic and abiotic stresses. Species distributed along a moisture gradient, such as Stipa purpurea, a dominant grass in alpine arid and semi-arid meadows on the Tibetan Plateau, provide an opportunity to evaluate the effects of long-term adaptation to differing degrees o...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-014-0419-7
更新日期：2015-05-01 00:00:00
