Illumina-based transcriptomic analysis of the fast-growing leguminous tree : functional gene annotation and identification of novel SSR-markers.

is a fast-growing leguminous tree that is widely cultivated in tropical areas such as Indonesia, Malaysia, Australia, and southern China. This tree has versatile utility in timber, furniture, and pulp production. Illumina sequencing of was conducted, and the raw data of 124,410,892 reads were filtered and assembled into 93,317 unigenes, with a total of 84,411,793 bases.

Comparative RNA-Seq analysis of the root revealed transcriptional regulation system for aluminum tolerance in contrasting indica rice of North East India.

Expression pattern of aluminum (Al) tolerance genes is one of the major determinants of Al avoidance/tolerance within plant cultivars. We have performed transcriptome analysis of two contrasting (Al-tolerant, Disang; Al-sensitive, Joymati) cultivars of India's North Eastern region, an indica rice diversity hotspot, on exposure to excess Al treatment in acidic condition. Co-expression analysis and SNPs enrichment analysis proposed the role of both trans-acting and cis-acting polymorphisms in Al signaling in the Al-tolerant cultivar.

A single-population GWAS identified expression level polymorphism caused by promoter variants is associated with variation in aluminum tolerance in a local population.

Organic acids (OA) are released from roots in response to aluminum (Al), conferring an Al tolerance to plants that is regulated by OA transporters such as ALMT (Al-activated malate transporter) and multi-drug and toxic compound extrusion (MATE). We have previously reported that the expression level polymorphism (ELP) of is strongly associated with variation in Al tolerance among natural accessions of Arabidopsis. However, although is also expressed following Al exposure and contributes to Al tolerance, whether contributes to the variation of Al tolerance and the molecular mechanisms of ELP remains unclear.

Genome-Wide Association Study and Genomic Prediction Elucidate the Distinct Genetic Architecture of Aluminum and Proton Tolerance in .

Under acid soil conditions, Al stress and proton stress can occur, reducing root growth and function. However, these stressors are distinct, and tolerance to each is governed by multiple physiological processes. To better understand the genes that underlie these coincidental but experimentally separable stresses, a genome-wide association study (GWAS) and genomic prediction (GP) models were created for approximately 200 diverse accessions.

Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to HO.

Hydrogen peroxide (HO) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of HO in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by HO application in Arabidopsis () seedlings.

Comparative genome-wide analysis of WRKY transcription factors in two Asian legume crops: Adzuki bean and Mung bean.

The seminal participation of WRKY transcription factors in plant development, metabolism and in the governance of defense mechanism implicated their gaining importance for genomic and functional studies. The recent release of draft genome sequences of two legume crops, Adzuki bean (Vigna angularis) and Mung bean (Vigna radiata) has paved the way for characterization of WRKY gene family in these crops. We found 84 WRKY genes in Adzuki bean (VaWRKY) and 85 WRKY genes in Mung bean (VrWRKY).

Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags.

Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.

Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis.

In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of '4 bases-a spacer with a flexible length-4 bases'.

Plant Promoter Database (PPDB).

ppdb ( http://ppdb.agr.gifu-u.

Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance.

Differences in the expression levels of aluminium (Al) tolerance genes are a known determinant of Al tolerance among plant varieties. We combined transcriptomic analysis of six Arabidopsis thaliana accessions with contrasting Al tolerance and a reverse genetic approach to identify Al-tolerance genes responsible for differences in Al tolerance between accession groups. Gene expression variation increased in the signal transduction process under Al stress and in growth-related processes in the absence of stress.

Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana.

Plants have evolved a series of tolerance mechanisms to saline stress, which perturbs physiological processes throughout the plant. To identify genetic mechanisms associated with salinity tolerance, we performed linkage analysis and genome-wide association study (GWAS) on maintenance of root growth of Arabidopsis thaliana in hydroponic culture with weak and severe NaCl toxicity. The top 200 single-nucleotide polymorphisms (SNPs) determined by GWAS could cumulatively explain approximately 70% of the variation observed at each stress level.