Abstract:
BACKGROUND:Ramie (Boehmeria nivea L.), popularly known as "China grass", is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remains unknown. RESULTS:A whole sequencing run was performed on the 454 GS FLX + platform using four separately pooled parts of ramie bast. This generated 1,030,057 reads with an average length of 457 bp. Among the 58,369 unigenes (13,386 contigs and 44,983 isotigs) that were generated through de novo assembly, 780 were differentially expressed. As a result, 13 genes that belong to the cellulose synthase gene family (four), the expansin gene family (three) and the xyloglucan endotransglucosylase/hydrolase (XTH) gene family (six) were up-regulated in the top part of the bast, which was in contrast to the other three parts. The identification of these 13 concurrently up-regulated unigenes indicated that the early stage (represented by the top part of the bast) might be important for the molecular regulation of ramie fiber development. Further analysis indicated that four of the 13 unigenes from the expansin (two) and XTH (two) families shared a coincident expression pattern during the whole growth season, which implied they were more relevant to ramie fiber development (fiber quality, etc.) during the different seasons than the other genes. CONCLUSIONS:To the best of our knowledge, this study is the first to characterize ramie fiber development at different developmental stages. The identified transcripts will improve our understanding of the molecular mechanisms involved in ramie fiber development. Moreover, the identified differentially expressed genes will accelerate molecular research on ramie fiber growth and the breeding of ramie with better fiber yields and quality.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Chen J,Pei Z,Dai L,Wang B,Liu L,An X,Peng Ddoi
10.1186/1471-2164-15-919subject
Has Abstractpub_date
2014-10-22 00:00:00pages
919issn
1471-2164pii
1471-2164-15-919journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina Methylation...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07168-8
更新日期:2020-10-27 00:00:00
abstract:BACKGROUND:Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. RESULTS:We selected 25 representative strains within 16 V. cholerae serogrou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5603-7
更新日期:2019-03-25 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:The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-91
更新日期:2013-02-11 00:00:00
abstract:BACKGROUND:The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda w...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-294
更新日期:2006-11-17 00:00:00
abstract:BACKGROUND:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1658-2
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Emerging evidence has been experimentally confirmed the tissue-specific expression of circRNAs (circRNAs). Global identification of human tissue-specific circRNAs is crucial for the functionality study, which facilitates the discovery of circRNAs for potential diagnostic biomarkers. RESULTS:In this study, c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4335-9
更新日期:2018-01-19 00:00:00
abstract:BACKGROUND:Transporter proteins are one of an organism's primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S1-S8
更新日期:2011-06-15 00:00:00
abstract:BACKGROUND:Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES coverage of nucleotides in targeted regions are recognized, it is not well understood how repetition o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2107-y
更新日期:2015-11-25 00:00:00
abstract:BACKGROUND:The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-82
更新日期:2012-02-29 00:00:00
abstract:BACKGROUND:Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction betwe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1808-6
更新日期:2015-08-14 00:00:00
abstract:BACKGROUND:Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2534-4
更新日期:2016-03-14 00:00:00
abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-686
更新日期:2013-10-06 00:00:00
abstract:BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5827-6
更新日期:2019-05-30 00:00:00
abstract:BACKGROUND:Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-857
更新日期:2013-12-05 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:Prolactin is a polypeptide hormone secreted by the anterior pituitary gland that plays an essential role in lactation, tissue growth, and suppressing apoptosis to increase cell survival. Prolactin serves as a key player in many life-critical processes, including immune system and reproduction. Prolactin is a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2785-0
更新日期:2016-06-29 00:00:00
abstract:BACKGROUND:The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07287-2
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamica...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-520
更新日期:2013-07-30 00:00:00
abstract:BACKGROUND:Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-314
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4861-0
更新日期:2018-06-20 00:00:00
abstract:BACKGROUND:Protein and mRNA levels for several selenoproteins, such as glutathione peroxidase-1 (Gpx1), are down-regulated dramatically by selenium (Se) deficiency. These levels in rats increase sigmoidally with increasing dietary Se and reach defined plateaus at the Se requirement, making them sensitive biomarkers for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-26
更新日期:2011-01-12 00:00:00
abstract:BACKGROUND:Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutrit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-522
更新日期:2011-10-23 00:00:00
abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-188
更新日期:2012-05-15 00:00:00
abstract:BACKGROUND:Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cel...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4011-0
更新日期:2017-08-10 00:00:00
abstract:BACKGROUND:Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. RESULTS:In this study, 48 CIPK genes (SsCIPKs) were identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07264-9
更新日期:2020-12-07 00:00:00
abstract:BACKGROUND:The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-185
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic amino acids arginine and lysine, which results in functional maturation of the target protein. In vit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-618
更新日期:2011-12-20 00:00:00
abstract:BACKGROUND:Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis, as it catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5728-8
更新日期:2019-05-22 00:00:00
abstract:BACKGROUND:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-77
更新日期:2014-01-28 00:00:00