RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes.

Although many genes may serve as reference genes, they may cause different expression patterns by selecting different reference genes because no single gene is expressed consistently in all tested tissues of an organism under all environmental and developmental conditions. Thus, it is becoming increasingly important and necessary to identify suitable reference genes before performing gene expression analysis. Currently, there are several computational tools available for evaluating the stability of candidate reference genes.

Evaluation of reference genes for miRNA and mRNA normalization in tobacco infected with PVY, PVY and PVY-NTN strains.

This is the first report on identification of the most suitable reference genes for RT-qPCR quantification of miRNA and mRNA in tobacco response to the prevalent recombinant potato virus Y (PVY) strains PVY, PVY and the newly identified PVY-NTN. Of 10 tested genes, the expression levels of neIF5C, nU2af and nPP2A were the most stable in samples taken from non-inoculated, mock-inoculated, and infected plants at three days post-inoculation (dpi) and 14 dpi. While the homologues of eIF5 were most stably expressed in tobacco in this study and in potato in our previous study (Yin et al.

Reference gene selection for miRNA and mRNA normalization in potato in response to potato virus Y.

This was the first report on evaluating candidate reference genes for quantifying the expression profiles of both coding (e.g., mRNA) and non-coding (e.

High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in .

This study sought novel ionizing radiation-response (IR-response) genes in (). was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced.

microRNA response in potato virus Y infected tobacco shows strain-specificity depending on host and symptom severity.

The present study demonstrates how different potato virus Y (PVY) strains affect the miRNA balance in tobacco cv. Samsun. The two prevalent strains PVY and PVY caused severe and mild veinal necrosis (VN) respectively, and the unique PVY-NTN strain induced milder vein clearing (VCl) in the upper non-inoculated leaves.

Genome of wild olive and the evolution of oil biosynthesis.

Here we present the genome sequence and annotation of the wild olive tree ( var. ), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map.

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.

Background: Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield.

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii.

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton.

A cotton miRNA is involved in regulation of plant response to salt stress.

The present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target gene GhCHR from cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting that GhCHR encodes a zinc-finger domain-containing transcription factor.

Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing.

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.

Small RNA sequencing identifies miRNA roles in ovule and fibre development.

MicroRNAs (miRNAs) have been found to be differentially expressed during cotton fibre development. However, which specific miRNAs and how they are involved in fibre development is unclear. Here, using deep sequencing, 65 conserved miRNA families were identified and 32 families were differentially expressed between leaf and ovule.

microRNA evolution and expression analysis in polyploidized cotton genome.

Cotton (Gossypium hirsutum L.), the most important fibre plant in the world, is a tetraploid species, originating from the reunion of two ancestral cotton species ~1-2 million years ago. It has been reported that a great number of genes were quickly erased or preferentially remained after whole-genome duplication, ultimately leading to morphogenesis evolution.

Global microRNA modification in cotton (Gossypium hirsutum L.).

MicroRNAs (miRNAs) are small noncoding RNAs participating in versatile biological processes via post-transcriptionally gene regulation. However, how miRNAs are modified or degraded remains unknown, despite years of studies have unravelled much details of miRNA biogenesis and function. Here, we systematically investigated miRNA modification using six small RNA sequencing libraries generated from cotton seedling as well as cotton fibre at five developmental stages.

Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton.

Drought and salinity are two major environmental factors adversely affecting plant growth and productivity. However, the regulatory mechanism is unknown. In this study, the potential roles of small regulatory microRNAs (miRNAs) in cotton response to those stresses were investigated.

Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii.

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play versatile functions in multiple aspects of plant growth and development. However, no systematical study has been performed in cotton. In this study, we performed for the first time the genome-wide identification and expression analysis of the TCP transcription factor family in Gossypium raimondii.

Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431.

Background: Paclitaxel (Taxol™) is an important anticancer drug with a unique mode of action. The biosynthesis of paclitaxel had been considered restricted to the Taxus species until it was discovered in Taxomyces andreanae, an endophytic fungus of T. brevifolia.

Expression of microRNAs and their targets regulates floral development in tobacco (Nicotiana tabacum).

MicroRNAs (miRNAs) are an extensive class of endogenous posttranscriptional gene regulators that function to mediate gene expression by cleaving target mRNAs or by preventing protein translation. Because of their importance in mediating gene regulation, identifying and elucidating the function of miRNAs have been the primary focus of many researchers. Now that many miRNAs have been identified and assessed for their functionality, the next step is to create expression profiles for miRNAs, so that gene expression studies can be further enhanced with knowledge of the basal expression levels of miRNAs and their targets.

High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress.

MicroRNAs (miRNAs) are an important class of small regulatory RNAs. The goal of this study was to analyse stress-responsive miRNAs in switchgrass (Panicum virgatum), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt- and drought-treated switchgrass using Illumina sequencing technology, we identified 670 known miRNA families from a total of more than 50 million short reads.

Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate.

Background: Plant cell culture represents an alternative source for producing high-value secondary metabolites including paclitaxel (Taxol®), which is mainly produced in Taxus and has been widely used in cancer chemotherapy. The phytohormone methyl jasmonate (MeJA) can significantly increase the production of paclitaxel, which is induced in plants as a secondary metabolite possibly in defense against herbivores and pathogens. In cell culture, MeJA also elicits the accumulation of paclitaxel; however, the mechanism is still largely unknown.

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs.

miRDeepFinder is a software package developed to identify and functionally analyze plant microRNAs (miRNAs) and their targets from small RNA datasets obtained from deep sequencing. The functions available in miRDeepFinder include pre-processing of raw data, identifying conserved miRNAs, mining and classifying novel miRNAs, miRNA expression profiling, predicting miRNA targets, and gene pathway and gene network analysis involving miRNAs. The fundamental design of miRDeepFinder is based on miRNA biogenesis, miRNA-mediated gene regulation and target recognition, such as perfect or near perfect hairpin structures, different read abundances of miRNA and miRNA*, and targeting patterns of plant miRNAs.

De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome.

High-throughput RNA sequencing was performed for comprehensively analyzing the transcriptome of the purple sweet potato. A total of 58,800 unigenes were obtained and ranged from 200 nt to 10,380 nt with an average length of 476 nt. The average expression of one unigene was 34 reads per kb per million reads (RPKM) with a maximum expression of 1,935 RPKM.

Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database.

A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members.

Transcriptome-wide identification and stress properties of the 14-3-3 gene family in cotton (Gossypium hirsutum L.).

14-3-3s are a class of conserved proteins in eukaryotes involved in almost all cellular processes. Published studies have shown that this family plays a role in response to stress conditions. In this study, comparative genomics identified thirty-one 14-3-3 cDNAs encoding 25 unique proteins with transcripts that were sufficiently divergent in the coding regions to define different 14-3-3 members.

In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species.

MicroRNAs are a recently identified class of small regulatory RNAs that target more than 30% protein-coding genes. Elevating evidence shows that miRNAs play a critical role in many biological processes, including developmental timing, tissue differentiation, and response to chemical exposure. In this study, we applied a computational approach to analyze expressed sequence tags, and identified 32 miRNAs belonging to 22 miRNA families, in three earthworm species Eisenia fetida, Eisenia andrei, and Lumbricus rubellus.

Target-align: a tool for plant microRNA target identification.

Motivation: MicroRNAs (miRNAs) are important regulatory molecules. A critical step in elucidating miRNA function is identifying potential miRNA targets. However, few reliable tools have been developed for identifying miRNA targets in plants.