Genomic Responses Associated with Drought Stress in Walnut as Revealed Transcriptome Sequencing

Walnut production is challenged by abiotic stresses. We investigated the leaf transcriptome responses of walnut under control and drought stress in 9 and 18 days. We identified 921, 1035 differentially expressed genes (DEGs) between control and drought stress groups in 9 and 18-day, respectively. In control and drought stress conditions DEGs were significantly enriched into the abscisic acid biosynthesis, regulation of stomata closure, leaf morphogenesis, carbohydrate metabolism, oxidative stress, cell wall macromolecule catabolism, and secondary metabolite biosynthesis pathways. We confirmed our RNA-Seq data using quantitative real-time PCR (qPCR) of six candidate genes. Our results indicated that more complicated transcript regulation of drought responses following prolong exposure to drought stress. In general, walnut activated more tolerance mechanisms 18 days after drought stress. Findings of this research would be useful for future studies on breeding for drought tolerance of Persian walnut and related species.

De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Leaf Transcriptome Analysis of Broomcorn Millet Uncovers Key Genes and Pathways in Response to Sporisorium destruens

Broomcorn millet (Panicum miliaceum L.) affected by smut (caused by the pathogen Sporisorium destruens) has reduced production yields and quality. Determining the tolerance of broomcorn millet varieties is essential for smut control. This study focuses on the differences in the phenotypes, physiological characteristics, and transcriptomes of resistant and susceptible broomcorn millet varieties under Sporisorium destruens stress. In diseased broomcorn millet, the plant height and stem diameter were reduced, while the number of nodes increased. After infection, the activities of superoxide dismutase and peroxidase decreased, and malondialdehyde and relative chlorophyll content (SPAD) decreased. Transcriptome analysis showed 514 and 5452 differentially expressed genes (DEGs) in the resistant and susceptible varieties, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that pathways related to plant disease resistance, such as phenylpropanoid biosynthesis, plant–pathogen interaction, and plant hormone signal transduction, were significantly enriched. In addition, the transcriptome changes of cluster leaves and normal leaves in diseased broomcorn millet were analysed. Gene ontology and KEGG enrichment analyses indicated that photosynthesis played an important role in both varieties. These findings lay a foundation for future research on the molecular mechanism of the interaction between broomcorn millet and Sporisorium destruens.

Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon.

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequence complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome, which demonstrate that many genes are absent from the reference genomes whose analysis has dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and investigated network topology and differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable occupancy in the pan-genome (genes which are either present in all studied genotypes or missing in some genotypes) show different distributions among co-expression modules. Co-expression analysis united drought genes expressed in drought-stressed plants into 9 modules covering 343 hub genes (440 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 724 hub genes (911 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Characterizing the Leaf Transcriptome of Chrysanthemum rhombifolium (Ling et C. Shih), a Drought Resistant, Endemic Plant From China

Chrysanthemum rhombifolium (Ling et C. Shih), an endemic plant that is extremely well-adapted to harsh environments. However, little is known about its molecular biology of the plant's resistant traits against stress, or even its molecular biology of overall plant. To investigate the molecular biology of C. rhombifolium and mechanism of stress adaptation, we performed transcriptome sequencing of its leaves using an Illumina platform. A total of 130,891 unigenes were obtained, and 97,496 (~74.5%) unigenes were annotated in the public protein database. The similarity search indicated that 40,878 and 74,084 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Of these, 56,213 and 42,005 unigenes were assigned to the Gene Ontology (GO) database and Cluster of Orthologous Groups (COG), respectively, and 38,918 unigenes were mapped into five main categories, including 18 KEGG pathways. Metabolism was the largest category (23,128, 59.4%) among the main KEGG categories, suggesting active metabolic processes in C. rhombifolium. About 2,459 unigenes were annotated to have a role in defense mechanism or stress tolerance. Transcriptome analysis of C. rhombifolium revealed the presence of 12,925 microsatellites in 10,524 unigenes and mono, trip, and dinucleotides having higher polymorphism rates. The phylogenetic analysis based on GME gene among related species confirmed the reliability of the transcriptomic data. This work is the first genetic study of C. rhombifolium as a new plant resource of stress-tolerant genes. This large number of transcriptome sequences enabled us to comprehensively understand the basic genetics of C. rhombifolium and discover novel genes that will be helpful in the molecular improvement of chrysanthemums.

Ethephon Activates the Transcription of Senescence-Associated Genes and Nitrogen Mobilization in Grapevine Leaves (Vitis vinifera cv. Riesling)

Nitrogen (N) remobilization in the context of leaf senescence is of considerable importance for the viability of perennial plants. In late-ripening crops, such as Vitis vinifera, it may also affect berry ripening and fruit quality. Numerous studies on the model plant Arabidopsis thaliana have confirmed an involvement of the plant hormone ethylene in the regulation of senescence. However, ethylene research on grapevine was mostly focused on its involvement in berry ripening and stress tolerance until now. To investigate the effect of ethylene on the initiation, regulation, and progress of senescence-dependent N mobilization in grapevine leaves, we treated field-grown Vitis vinifera cv. Riesling vines with 25 mM ethephon at the end of berry ripening. Ethephon induced premature chlorophyll degradation and caused a shift of the leaf transcriptome equivalent to developmental leaf senescence. The upregulated metabolic processes covered the entire N remobilization process chain, altered the amino acid composition in the leaves, and resulted in an average 60% decrease in leaf N. Our findings increase the fundamental knowledge about the initiation and manipulation of leaf N remobilization in perennial woody plants by ethephon. This offers a methodological approach to the targeted induction of senescence and thus to an improvement in the N supply of grapes.

Molecular cloning and characterization of GhERF105, a gene contributing to the regulation of gland formation in Upland cotton (Gossypium hirsutum L.)

Background: Upland cotton ( Gossypium hirsutum L.) is one of the most economically important crops worldwide . Cottonseed is a major significant source of fiber, feed, foodstuff, oil and biofuel products. However, the utilization of cottonseed is limited by the presence of small and darkly pigmented glands that contain large amounts of gossypol, which is toxic to human beings and other non-ruminant animals. To date,some progress has been made in the pigment gland formation, but the underlying molecular mechanism of pigment gland formation was still unclear. Results: In this study, we identified an AP2/ERF transcription factor named GhERF105 (Gh_A12G1784), which is involved in the regulation of gland pigmentation, from comparative transcriptome analysis of the leaf transcriptome from two pairs of glanded and glandless accessions, which are CCRI12 and CCRI12XW, L7 and L7XW. This gene encoded an ERF protein containing a converved AP2 domain localized in the nucleus with transcriptional activity., and it showed the high expression in glanded cotton accessions that contained much gossypol. Virus-induced gene silencing(VIGS) against GhERF105 caused the dramatic reduction in the number of glands and significantly lowered levels of gossypol in cotton leaves. GhERF105 showed the patterns of spatiotemporal and inducible expression in the glanded plants. Conclusions: These results suggest that GhERF105 contributes to the pigment gland formation and gossypol biosynthesis in partial organs of glanded plant. It also provides a potential molecular basis to generate ‘glandless-seed’ and ‘glanded-plant’ cotton cultivar.