Abstract:
BACKGROUND:Auxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which auxin regulate the process of adventitious rooting are less well known. RESULTS:The RNA-Seq data analysis indicated that IBA treatment greatly increased the amount of clean reads and the amount of expressed unigenes by 24.29 % and 27.42 % and by 4.3 % and 5.04 % at two time points, respectively, and significantly increased the numbers of unigenes numbered with RPKM = 10-100 and RPKM = 500-1000 by 13.04 % and 3.12 % and by 24.66 % and 108.2 % at two time points, respectively. Gene Ontology (GO) enrichment analysis indicated that the enrichment of down-regulated GOs was 2.87-fold higher than that of up-regulated GOs at stage 1, suggesting that IBA significantly down-regulated gene expression at 6 h. The GO functional category indicated that IBA significantly up- or down-regulated processes associated with auxin signaling, ribosome assembly and protein synthesis, photosynthesis, oxidoreductase activity and extracellular region, secondary cell wall biogenesis, and the cell wall during the development process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that ribosome biogenesis, plant hormone signal transduction, pentose and glucuronate interconversions, photosynthesis, phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, ribosome, cutin, flavonoid biosynthesis, and phenylalanine metabolism were the pathways most highly regulated by IBA. A total of 6369 differentially expressed (2-fold change > 2) unigenes (DEGs) with 3693 (58 %) that were up-regulated and 2676 (42 %) down-regulated, 5433 unigenes with 2208 (40.6 %) that were up-regulated and 3225 (59.4 %) down-regulated, and 7664 unigenes with 3187 (41.6 %) that were up-regulated and 4477 (58.4 %) down-regulated were detected at stage 1, stage 2, and between stage 1 and stage 2, respectively, suggesting that IBA treatment increased the number of DEGs. A total of 143 DEGs specifically involved in plant hormone signaling and 345 transcription factor (TF) genes were also regulated by IBA. qRT-PCR validation of the 36 genes with known functions indicated a strong correlation with the RNA-Seq data. CONCLUSIONS:The changes in GO functional categories, KEGG pathways, and global DEG profiling during adventitious rooting induced by IBA were analyzed. These results provide valuable information about the molecular traits of IBA regulation of adventitious rooting.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Li SW,Shi RF,Leng Y,Zhou Ydoi
10.1186/s12864-016-2372-4subject
Has Abstractpub_date
2016-01-12 00:00:00pages
43issn
1471-2164pii
10.1186/s12864-016-2372-4journal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an improved understanding of miRNAs will further our knowledge of these networks. There is a many-to-many ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-138
更新日期:2011-03-06 00:00:00
abstract:BACKGROUND:Bacillus pumilus is a Gram-positive and endospore-forming bacterium broadly existing in a variety of environmental niches. Because it produces and secrets many industrially useful enzymes, a lot of studies have been done to understand the underlying mechanisms. Among them, scoC was originally identified as a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5671-8
更新日期:2019-04-30 00:00:00
abstract:BACKGROUND:ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4559-3
更新日期:2018-03-01 00:00:00
abstract:BACKGROUND:Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on ho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6102-6
更新日期:2019-10-22 00:00:00
abstract:BACKGROUND:The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1867-8
更新日期:2015-09-02 00:00:00
abstract:BACKGROUND:Many transcripts have been generated due to the development of sequencing technologies, and lncRNA is an important type of transcript. Predicting lncRNAs from transcripts is a challenging and important task. Traditional experimental lncRNA prediction methods are time-consuming and labor-intensive. Efficient ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07237-y
更新日期:2020-12-17 00:00:00
abstract:BACKGROUND:S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-523
更新日期:2013-07-31 00:00:00
abstract:BACKGROUND:The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the exploration of the mechanisms underlying genome plasticity. The family Vibrionaceae is found in the Gammapr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S1-S11
更新日期:2009-07-07 00:00:00
abstract:BACKGROUND:Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-468
更新日期:2010-08-11 00:00:00
abstract:BACKGROUND:High throughput experiments resulted in many genomic datasets and hundreds of candidate disease genes. To discover the real disease genes from a set of candidate genes, computational methods have been proposed and worked on various types of genomic data sources. As a single source of genomic data is prone of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S7-S27
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific tr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-161
更新日期:2010-03-09 00:00:00
abstract:BACKGROUND:The establishment of C4 photosynthesis in maize is associated with differential accumulation of gene transcripts and proteins between bundle sheath and mesophyll photosynthetic cell types. We have physically separated photosynthetic cell types in the leaf blade to characterize differences in gene expression ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-12
更新日期:2007-01-09 00:00:00
abstract:BACKGROUND:Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally chal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-478
更新日期:2014-06-17 00:00:00
abstract:BACKGROUND:Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-214
更新日期:2007-07-04 00:00:00
abstract:BACKGROUND:Host-specific environmental factors induce changes in Bacillus anthracis gene transcription during infection. A global transcription regulator, CodY, plays a pivotal role in regulating central metabolism, biosynthesis, and virulence in B. anthracis. In this study, we utilized RNA-sequencing to assess changes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3004-8
更新日期:2016-08-17 00:00:00
abstract:BACKGROUND:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-325
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Drug resistance has become a severe challenge for treatment of HIV infections. Mutations accumulate in the HIV genome and make certain drugs ineffective. Prediction of resistance from genotype data is a valuable guide in choice of drugs for effective therapy. RESULTS:In order to improve the computational pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S5-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. RESUL...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-491
更新日期:2008-10-17 00:00:00
abstract:BACKGROUND:The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inference...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2848-2
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecolo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1096
更新日期:2014-12-12 00:00:00
abstract:BACKGROUND:Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulating cell cycle progression and apoptosis both positively and negatively. However, it still remains to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-275
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism has been key to the evolution of the Hymenoptera, and particularly the social Hymenoptera where the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-623
更新日期:2011-12-20 00:00:00
abstract:BACKGROUND:Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgut proteins and their potential role in refractoriness for malaria control in Anopheles mosquitoes. T...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4729-3
更新日期:2018-05-08 00:00:00
abstract:BACKGROUND:Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3699-1
更新日期:2017-05-02 00:00:00
abstract:BACKGROUND:Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by inflammation and destruction of synovial joints. RA affects up to 1 % of the population worldwide. Currently, there are no drugs that can cure RA or achieve sustained remission. The unknown cause of the disease represents a significan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2910-0
更新日期:2016-08-22 00:00:00
abstract:BACKGROUND:Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome. RESULTS:Using empirical estimates of recombination rate across the human geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-146
更新日期:2007-06-06 00:00:00
abstract:BACKGROUND:Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS:This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, us...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3507-y
更新日期:2017-02-06 00:00:00
abstract:BACKGROUND:Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. With more and more complete genomes accomplished, lots of genomic comparisons have been conducted in order t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3655-0
更新日期:2017-03-29 00:00:00
abstract:BACKGROUND:The laying hen model of spontaneous epithelial ovarian cancer (EOC) is unique in that it is the only model that enables observations of early events in disease progression and is therefore also uniquely suited for chemoprevention trials. Previous studies on the effect of dietary flaxseed in laying hens have ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-709
更新日期:2014-08-24 00:00:00
abstract:BACKGROUND:Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. RESULTS:We have used array comparative genomic hybridization (aCGH)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-62
更新日期:2010-01-25 00:00:00