scholarly journals Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.

2020 ◽  
Vol 21 (21) ◽  
pp. 8148
Author(s):  
Stephanie Schaarschmidt ◽  
Axel Fischer ◽  
Lovely Mae F. Lawas ◽  
Rejbana Alam ◽  
Endang M. Septiningsih ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Stress Responses ◽  
De Novo ◽  
Oryza Sativa L ◽  
Cost Effective ◽  
Rna Seq ◽  
High Quality ◽  
Novel Transcript

The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.

scholarly journals Overexpression of OsABCG48 Lowers Cadmium in Rice (Oryza sativa L.)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 918
Author(s):  
Xingzhe Cai ◽  
Meng Wang ◽  
Yucong Jiang ◽  
Changhu Wang ◽  
David W. Ow
Keyword(s):  
Oryza Sativa L ◽  
Cost Effective ◽  
Health Issues ◽  
Rna Seq ◽  
Wild Type ◽  
Genetic Changes ◽  
Cd Accumulation ◽  
Lateral Root Development ◽  
Atp Binding Cassette Transporter ◽  
Cost Effective Approach

Cadmium pollution threatens food safety and security by causing health issues and reducing farmland availability. Engineering genetic changes in crop plants to lower Cd accumulation can be a cost-effective approach to address this problem. Previously, we reported that a rice line, 2B, which expresses a truncated version of OsO3L2 had reduced Cd accumulation throughout the plant, including in seed. However, downstream events caused by expression of this gene were not known. In this study, RNA-seq was used to identify differentially expressed genes between the wild type and 2B rice with or without Cd treatment, leading to the study of an ABC transporter gene, OsABCG48 (ATP-Binding Cassette transporter G family member 48). Heterologous expression of OsABCG48 conferred tolerance to Cd in Schizosaccharomyces pombe, Arabidopsis and rice. Moreover, overexpressing OsABCG48 in rice lowered root Cd accumulation that was associated with more extensive lateral root development. These data suggest that OsABCG48 might have applications for engineering low-Cd rice.

scholarly journals A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3702 ◽  
Author(s):  
Santiago Montero-Mendieta ◽  
Manfred Grabherr ◽  
Henrik Lantz ◽  
Ignacio De la Riva ◽  
Jennifer A. Leonard ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cost Effective ◽  
Model Organisms ◽  
Rna Seq ◽  
Assembly Pipeline ◽  
Wide Variability ◽  
History Of ◽  
Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

scholarly journals CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure

2021 ◽  
Vol 17 (11) ◽  
pp. e1009631
Author(s):  
Raquel Linheiro ◽  
John Archer
Keyword(s):  
De Novo ◽  
Simulated Data ◽  
Real Data ◽  
Gene Families ◽  
Classification Systems ◽  
Whole Body ◽  
Cdna Libraries ◽  
Sequence Information ◽  
Rna Seq ◽  
High Quality

With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene families present. As a demonstration of CStones ability to assemble high-quality contigs, and to label them in this manner, both simulated and real data were used. For simulated data, ten million read pairs were generated from cDNA libraries representing four species, Drosophila melanogaster, Panthera pardus, Rattus norvegicus and Serinus canaria. These were assembled using CStone, Trinity and rnaSPAdes; the latter two being high-quality, well established, de novo assembers. For real data, two RNA-Seq datasets, each consisting of ≈30 million read pairs, representing two adult D. melanogaster whole-body samples were used. The contigs that CStone produced were comparable in quality to those of Trinity and rnaSPAdes in terms of length, sequence identity of aligned regions and the range of cDNA transcripts represented, whilst providing additional information on chimerism. Here we describe the details of CStones assembly and classification process, and propose that similar classification systems can be incorporated into other de novo assembly tools. Within a related side study, we explore the effects that chimera’s within reference sets have on the identification of differentially expression genes. CStone is available at: https://sourceforge.net/projects/cstone/.

scholarly journals Investigation of a Novel Salt Stress-Responsive Pathway Mediated by Arabidopsis DEAD-Box RNA Helicase Gene AtRH17 Using RNA-Seq Analysis

2020 ◽  
Vol 21 (5) ◽  
pp. 1595 ◽  
Author(s):  
Hye-Yeon Seok ◽  
Linh Vu Nguyen ◽  
Doai Van Nguyen ◽  
Sun-Young Lee ◽  
Yong-Hwan Moon
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Rna Helicase ◽  
Rna Seq ◽  
Salt Stress Tolerance ◽  
Salt Stress Condition ◽  
Dead Box ◽  
Helicase Gene ◽  
Upregulated Genes

Previously, we reported that overexpression of AtRH17, an Arabidopsis DEAD-box RNA helicase gene, confers salt stress-tolerance via a pathway other than the well-known salt stress-responsive pathways. To decipher the salt stress-responsive pathway in AtRH17-overexpressing transgenic plants (OXs), we performed RNA-Sequencing and identified 397 differentially expressed genes between wild type (WT) and AtRH17 OXs. Among them, 286 genes were upregulated and 111 genes were downregulated in AtRH17 OXs relative to WT. Gene ontology annotation enrichment and KEGG pathway analysis showed that the 397 upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Taken together, our results suggest that a high AtRH17 expression confers salt stress-tolerance through a novel salt stress-responsive pathway involving nine genes, other than the well-known ABA-dependent and ABA-independent pathways.

scholarly journals Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.)

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0172515 ◽  
Author(s):  
Jauhar Ali ◽  
Jian-Long Xu ◽  
Yong-Ming Gao ◽  
Xiu-Fang Ma ◽  
Li-Jun Meng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Oryza Sativa L ◽  
Abiotic Stress Tolerance

scholarly journals Structure and expression analysis of seven salt-related ERF genes of Populus

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10206
Author(s):  
Juanjuan Huang ◽  
Shengji Wang ◽  
Xingdou Wang ◽  
Yan Fan ◽  
Youzhi Han
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Expression Pattern ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Critical Role ◽  
Plant Stress ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Go Annotation

Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.

scholarly journals Modulation of GmFAD3 expression alters responses to abiotic stress in soybean

2020 ◽  
Author(s):  
Ajay Singh ◽  
Mahesh Kumar ◽  
Susheel Raina ◽  
Milind Ratnaparkhe ◽  
Jagadish Rane ◽  
...  
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
Fatty Acid ◽  
Stress Tolerance ◽  
Salinity Stress ◽  
Stress Responses ◽  
Fatty Acid Desaturase ◽  
Stress Conditions ◽  
Omega 3 ◽  
Soybean Plants

FAD3 play important roles in modulating membrane fluidity in response to various abiotic stresses. However, a comprehensive analysis of FAD3 in drought, salinity and heat stress tolerance is lacking in soybean. The present study assessed the functional role of fatty acid desaturase 3 to abiotic stress responses in soybean. We used Bean Pod Mottle Virus -based vector to alter expression of Glycine max omega-3 fatty acid desaturase . Higher levels of recombinant BPMV-GmFAD3 transcripts were detected in overexpressing soybean plants. Overexpression of GmFAD3 in soybean resulted in increased levels of jasmonic acid and higher expression of GmWRKY54 as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants under drought and salinity stress conditions. FAD3 overexpressing plants showed higher levels of chlorophyll content, leaf SPAD value, relative water content, chlorophyll fluorescence, transpiration rate, carbon assimilation rate, proline content and also cooler canopy under drought and salinity stress conditions as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants. Results from current study revealed that GmFAD3 overexpressing soybean plants exhibited drought and salinity stress tolerance although tolerance to heat stress was reduced. On the other hand, soybean plants silenced for GmFAD3 exhibited tolerance to heat stress, but were vulnerable to drought and salinity stress

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