Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems.

Abstract:

BACKGROUND:Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar. RESULTS:Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome. CONCLUSIONS:Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Calviño M,Bruggmann R,Messing J

doi

10.1186/1471-2164-12-356

subject

Has Abstract

pub_date

2011-07-08 00:00:00

pages

356

issn

1471-2164

pii

1471-2164-12-356

journal_volume

12

pub_type

杂志文章
  • Response of the mosquito protein interaction network to dengue infection.

    abstract:BACKGROUND:Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequenc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-380

    authors: Guo X,Xu Y,Bian G,Pike AD,Xie Y,Xi Z

    更新日期:2010-06-16 00:00:00

  • Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq.

    abstract:BACKGROUND:Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1390-y

    authors: Chen J,Chen B,Zhang D

    更新日期:2015-03-10 00:00:00

  • Substrate-dependent gene regulation of self-assembled human MSC spheroids on chitosan membranes.

    abstract:BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-10

    authors: Yeh HY,Liu BH,Sieber M,Hsu SH

    更新日期:2014-01-05 00:00:00

  • SNP discovery by high-throughput sequencing in soybean.

    abstract:BACKGROUND:With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-469

    authors: Wu X,Ren C,Joshi T,Vuong T,Xu D,Nguyen HT

    更新日期:2010-08-11 00:00:00

  • Testis-Specific GTPase (TSG): An oligomeric protein.

    abstract:BACKGROUND:Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talking with different kinases and playing a role in cellular signaling. However, only a few Rab proteins ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3145-9

    authors: Kumar S,Lee HJ,Park HS,Lee K

    更新日期:2016-10-10 00:00:00

  • Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.

    abstract:BACKGROUND:Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-488

    authors: Ling Z,Kong J,Liu F,Zhu H,Chen X,Wang Y,Li L,Nelson KE,Xia Y,Xiang C

    更新日期:2010-09-07 00:00:00

  • Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions.

    abstract:BACKGROUND:At sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6185-0

    authors: Gloux A,Duclos MJ,Brionne A,Bourin M,Nys Y,Réhault-Godbert S

    更新日期:2019-11-07 00:00:00

  • Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.

    abstract:BACKGROUND:Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein components of non-coding ribonucleoprotein (ncRNP) particles by RNA interference (RNAi) may therefore aff...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-278

    authors: Aftab MN,He H,Skogerbø G,Chen R

    更新日期:2008-06-11 00:00:00

  • Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi.

    abstract:BACKGROUND:Haloquadratum walsbyi represents up to 80% of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid lib...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1794-8

    authors: Martin-Cuadrado AB,Pašić L,Rodriguez-Valera F

    更新日期:2015-08-13 00:00:00

  • Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae.

    abstract:BACKGROUND:Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone m...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-550

    authors: Deng Y,Dai X,Xiang Q,Dai Z,He C,Wang J,Feng J

    更新日期:2010-10-09 00:00:00

  • Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells.

    abstract:BACKGROUND:The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-deficient CD3+ T-cells, including CD4+ and CD8+ subsets, using Affymetrix microarrays. RESULTS:The lar...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-233

    authors: Blomberg KE,Boucheron N,Lindvall JM,Yu L,Raberger J,Berglöf A,Ellmeier W,Smith CE

    更新日期:2009-05-18 00:00:00

  • Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model.

    abstract:BACKGROUND:High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele freque...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-605

    authors: Yin BC,Li H,Ye BC

    更新日期:2008-12-16 00:00:00

  • Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma.

    abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-252

    authors: Diboun I,Wernisch L,Orengo CA,Koltzenburg M

    更新日期:2006-10-09 00:00:00

  • Genomic predictions combining SNP markers and copy number variations in Nellore cattle.

    abstract:BACKGROUND:Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not suff...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4787-6

    authors: Hay EHA,Utsunomiya YT,Xu L,Zhou Y,Neves HHR,Carvalheiro R,Bickhart DM,Ma L,Garcia JF,Liu GE

    更新日期:2018-06-05 00:00:00

  • Global gene expression profile progression in Gaucher disease mouse models.

    abstract:BACKGROUND:Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal functions are obscure. RESULTS:To elucidate this pathogenic pathway, de...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-20

    authors: Xu YH,Jia L,Quinn B,Zamzow M,Stringer K,Aronow B,Sun Y,Zhang W,Setchell KD,Grabowski GA

    更新日期:2011-01-11 00:00:00

  • Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations.

    abstract:BACKGROUND:Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-346

    authors: Yang HC,Wang PL,Lin CW,Chen CH,Chen CH

    更新日期:2012-07-28 00:00:00

  • Sequence-indexed mutations in maize using the UniformMu transposon-tagging population.

    abstract:BACKGROUND:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-116

    authors: Settles AM,Holding DR,Tan BC,Latshaw SP,Liu J,Suzuki M,Li L,O'Brien BA,Fajardo DS,Wroclawska E,Tseung CW,Lai J,Hunter CT 3rd,Avigne WT,Baier J,Messing J,Hannah LC,Koch KE,Becraft PW,Larkins BA,McCarty DR

    更新日期:2007-05-09 00:00:00

  • Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis.

    abstract:BACKGROUND:The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5784-0

    authors: Gonzalo MJ,Díaz A,Dhillon NPS,Reddy UK,Picó B,Monforte AJ

    更新日期:2019-06-03 00:00:00

  • Identification of microRNA-mRNA modules using microarray data.

    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

    authors: Jayaswal V,Lutherborrow M,Ma DD,Yang YH

    更新日期:2011-03-06 00:00:00

  • The pathogenic human Torsin A in Drosophila activates the unfolded protein response and increases susceptibility to oxidative stress.

    abstract:BACKGROUND:Dystonia1 (DYT1) dystonia is caused by a glutamic acid deletion (ΔE) mutation in the gene encoding Torsin A in humans (HTorA). To investigate the unknown molecular and cellular mechanisms underlying DYT1 dystonia, we performed an unbiased proteomic analysis. RESULTS:We found that the amount of proteins and ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1518-0

    authors: Kim AY,Seo JB,Kim WT,Choi HJ,Kim SY,Morrow G,Tanguay RM,Steller H,Koh YH

    更新日期:2015-04-23 00:00:00

  • Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection.

    abstract:BACKGROUND:Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IP...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6156-5

    authors: Ma X,Zhao X,Wang K,Tang X,Guo J,Mi M,Qi Y,Chang L,Huang Y,Tong D

    更新日期:2019-11-04 00:00:00

  • Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.

    abstract:BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1321-y

    authors: Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

    更新日期:2015-02-15 00:00:00

  • Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization.

    abstract:BACKGROUND:Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups. RESULTS:We investigated the molecular characteristics of genetic ch...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-305

    authors: Lee GY,Yang WI,Jeung HC,Kim SC,Seo MY,Park CH,Chung HC,Rha SY

    更新日期:2007-09-03 00:00:00

  • Coevolution of paired receptors in Xenopus carcinoembryonic antigen-related cell adhesion molecule families suggests appropriation as pathogen receptors.

    abstract:BACKGROUND:In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3279-9

    authors: Zimmermann W,Kammerer R

    更新日期:2016-11-16 00:00:00

  • The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins.

    abstract:BACKGROUND:An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i) the bromodomain, which can recognize certain acetylation marks and (ii) the chromodomain, which can recognize certain meth...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-6

    authors: Perry J

    更新日期:2006-01-16 00:00:00

  • MetaTopics: an integration tool to analyze microbial community profile by topic model.

    abstract:BACKGROUND:Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3257-2

    authors: Yan J,Chuai G,Qi T,Shao F,Zhou C,Zhu C,Yang J,Yu Y,Shi C,Kang N,He Y,Liu Q

    更新日期:2017-01-25 00:00:00

  • Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors.

    abstract:BACKGROUND:Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity....

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-270

    authors: Cantu D,Segovia V,MacLean D,Bayles R,Chen X,Kamoun S,Dubcovsky J,Saunders DG,Uauy C

    更新日期:2013-04-22 00:00:00

  • Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain.

    abstract:BACKGROUND:Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4594-0

    authors: Herb BR,Shook MS,Fields CJ,Robinson GE

    更新日期:2018-03-26 00:00:00

  • UDiTaS™, a genome editing detection method for indels and genome rearrangements.

    abstract:BACKGROUND:Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4561-9

    authors: Giannoukos G,Ciulla DM,Marco E,Abdulkerim HS,Barrera LA,Bothmer A,Dhanapal V,Gloskowski SW,Jayaram H,Maeder ML,Skor MN,Wang T,Myer VE,Wilson CJ

    更新日期:2018-03-21 00:00:00

  • Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic ev

    abstract:BACKGROUND:Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adapta...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4487-2

    authors: Klonowska A,Melkonian R,Miché L,Tisseyre P,Moulin L

    更新日期:2018-01-30 00:00:00