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, 16,552 genes were expressed in all samples tested, probably representing the core component of the transcriptome. Twenty of the most abundant genes accounted for 12.7% of the sequences from the transcriptome. A 164-h infection seemingly induced a minor change in the transcriptome (162 genes). Additionally, a total of 162,412 splice junctions were identified. Among them, 1,164 appeared unique to 1 of the 2 groups: 868 splice junctions were observed only in infected animals, while 278 were only present in all 4 control animals. Biological functions associated with muscle contraction were predominant Gene Ontology terms enriched in the genes differentially expressed by infection. The primary function of two of the four regulatory networks impacted was related to skeletal and muscular systems. A total of 34 pathways were significantly impacted by infection. Several pathways were directly related to host immune responses, such as acute phase response, leukocyte extravasation, and antigen presentation, consistent with previous findings. Calcium signaling and actin cytoskeleton signaling were among the pathways most significantly impacted by infection in the bovine jejunum. Together, these data suggest that smooth muscle hypercontractility may be initiated as a result of a primary C. oncophora infection, which may represent a mechanism for host responses in the jejunum during nematode infection.
journal_name
Funct Integr Genomicsjournal_title
Functional & integrative genomicsauthors
Li RW,Schroeder SGdoi
10.1007/s10142-011-0259-7subject
Has Abstractpub_date
2012-03-01 00:00:00pages
35-44issue
1eissn
1438-793Xissn
1438-7948journal_volume
12pub_type
杂志文章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：:Control of proteolysis is important for plant growth, development, responses to stress, and defence against insects and pathogens. Members of the serpin protein family are likely to play a critical role in this control through irreversible inhibition of endogenous and exogenous target proteinases. Serpins have been fo...
journal_title：Functional & integrative genomics
pub_type： 杂志文章,评审
doi：10.1007/s10142-007-0059-2
更新日期：2008-02-01 00:00:00
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：:Jatropha curcas is a new promising bioenergy crop due to the high oil content in its seeds that can be converted into biodiesel. Seed size, a major determinant of Jatropha oil yield, is a target trait for Jatropha breeding. Due to the vital roles of phytohormone auxin in controlling seed and fruit development, we scre...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-014-0400-5
更新日期：2014-12-01 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：: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：: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：:Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we ...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-017-0575-7
更新日期：2018-01-01 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：: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：:MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. In this study, we investigate miRNAs in an agronomically important common tobacco in China, named Honghua Dajinyuan (a drought-tolerant cultivar). Here, we report a comprehensive analysis of miRNA expression profile...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-014-0365-4
更新日期：2014-06-01 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：: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：:The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the ap...
journal_title：Functional & integrative genomics
pub_type： 杂志文章
doi：10.1007/s10142-017-0559-7
更新日期：2017-07-01 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：: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：: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：: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 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：: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：: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：: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：: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：: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 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：: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：: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
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：: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
