Effect of choline amino acid ionic liquids on maize seed germination and endogenous plant hormone levels.

Prior research has established choline-based ionic liquids (ILs) as safe for various organisms. However, their impact on plants has been underexplored. To identify effective eco-friendly ILs, we synthesized seven choline amino acid ([Chl][AA]) ILs and analyzed their physiological influence on maize seed germination.

Effects of pyridinium-based ionic liquids with different alkyl chain lengths on the growth of maize seedlings.

The effects of four water-soluble pyridinium-based ionic liquids (ILs) differing in alkyl side chain length, namely, N-ethyl pyridinium bromide ([EPy]Br), N-butyl pyridinium bromide ([BPy]Br), N-hexyl pyridinium bromide ([HPy]Br), and N-octyl pyridinium bromide ([OPy]Br), on the growth of maize seedlings were investigated for the first time. The results revealed that the phytotoxicity of these ILs was significantly correlated with their concentration and alkyl side chain length. The 8-day 50% inhibition values indicated that the toxicity increased as the length of the alkyl chain increased: [EPy]Br < [BPy]Br < [HPy]Br < [OPy]Br.

Transcriptomic analysis of the phytotoxic effects of 1-allyl-3-methylimidazolium chloride on the growth and plant hormone metabolic pathways of maize (Zea mays L.) seedlings.

In this study, we investigated the phytotoxicity of an imidazolium-based ionic liquid, 1-allyl-3-methylimidazolium chloride ([Amim]Cl), against maize seedlings. It was found that in response to an increase in [Amim]Cl treatment concentrations, there were significant decreases in growth parameters (fresh weights and lengths) and the photosynthetic pigment contents of maize plants, whereas in contrast, the malondialdehyde content increased. In order to determine the molecular basis of [Amim]Cl-induced plant growth inhibition, an RNA-Seq analysis to examine the gene expression profiles of selected central biological pathways was performed.

Evolution of the RNA -Methyladenosine Methylome Mediated by Genomic Duplication.

RNA -methyladenosine (mA) modification is the most abundant form of RNA epigenetic modification in eukaryotes. Given that mA evolution is associated with the selective constraints of nucleotide sequences in mammalian genomes, we hypothesize that mA evolution can be linked, at least in part, to genomic duplication events in complex polyploid plant genomes. To test this hypothesis, we presented the maize () mA modification landscape in a transcriptome-wide manner and identified 11,968 mA peaks carried by 5,893 and 3,811 genes from two subgenomes (maize1 and maize2, respectively).

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.

A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, resulting in the loss of significant biological information and insights. To fill this gap, we present Comprehensive Assembly and Functional annotation of Unmapped RNA-Seq data (CAFU), a Galaxy-based framework that can facilitate the large-scale analysis of unmapped RNA sequencing (RNA-Seq) reads from single- and mixed-species samples.

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture.

DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation.

Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways.

DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation.

Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47.

A large-scale bioinformatics analysis revealed the origin and evolution of GT47 gene family, and identified two clades of intron-poor genes with putative functions in drought stress responses and seed development in maize. Glycosyltransferase family 47 (GT47) genes encode β-galactosyltransferases and β-glucuronyltransferases that synthesize pectin, xyloglucans and xylan, which are important components of the plant cell wall. In this study, we performed a systematic and large-scale bioinformatics analysis of GT47 gene family using 352 GT47 proteins from 15 species ranging from cyanobacteria to seed plants.

A systems approach to a spatio-temporal understanding of the drought stress response in maize.

Crops are often subjected to periods of drought stress during their life cycle. However, how stress response mechanisms contribute to the crosstalk between stress signaling pathways and developmental signaling pathways is still unknown. We built a gene co-expression network from a spatio-temporal transcriptomic map of the drought stress response in maize (Zea mays), profiled from three tissues and four developmental stages and characterized hub genes associated with duplication events, selection, and regulatory networks.

Identification of maize long non-coding RNAs responsive to drought stress.

Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed to shorter miRNAs and siRNAs. Emerging evidence shows that lncRNAs participate in stress responsive regulation. In this study, to identify the putative maize lncRNAs responsive to drought stress, 8449 drought responsive transcripts were first uploaded to the Coding Potential Calculator website for classification as protein coding or non-coding RNAs, and 1724 RNAs were identified as potential non-coding RNAs.

Functional analysis of the 5' regulatory region of the maize GALACTINOL SYNTHASE2 gene.

Maize (Zea mays) GALACTINOL SYNTHASE (GolS) is a key enzyme in the raffinose biosynthetic pathway. We have previously characterized the maize GolS2 (ZmGolS2) gene as heat shock induced in maize germinating seeds and cultured cells. Here we report the identification, isolation and characterization of the 1.

Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives.

Although plant resistance (R) genes are extremely diverse and evolve rapidly, little is known about the mechanisms that generate this sequence divergence. To investigate these forces, we compared all nucleotide binding sites and leucine-rich repeat R-genes between two closely related species, Arabidopsis thaliana and Arabidopsis lyrata. Our analyses revealed two distinct evolutionary patterns driven by either positive or stabilizing selection.

Structural and expressional analysis of the B-hordein genes in Tibetan hull-less barley.

The B-hordein gene family was analyzed from two Tibetan hull-less barley cultivars Z09 and Z26 (Hordeum vulgare subsp. vulgare). Fourteen B-hordein genes, designated BZ09-2 to BZ09-5 (from Z09) and BZ26-1 to BZ26-10 (from Z26), were sequenced.

Cloning and characterization of four B-hordein genes from Tibetan hull-less barley (Hordeum vulgare subsp. vulgare).

Four B-hordein genes, designated BH1-BH4, were cloned using PCR amplification from two hull-less barley cultivars, ZQ7239 and ZQ148, collected from Tibet. The results of sequencing indicated that BH1-BH4 contained complete open reading frames (ORFs). Comparison of their predicted polypeptide sequences with the published sequences suggested that they all share the same basic protein structure.