scholarly journals Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec

2020 ◽  
Vol 35 (1-2) ◽  
Author(s):  
Sarika Jaiswal ◽  
Aamir Khan ◽  
Johnson George K ◽  
Rahul Singh Jasrotia ◽  
U B Angadi ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Mosaic Disease ◽  
Whole Genome Sequence ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Web Resource ◽  
Elettaria Cardamomum ◽  
Molecular Events ◽  
Genomic Resource

Small cardamom (Elettaria cardamomum), is one of the costliest spices across the globe. It is grown in limited coastal tropical countries. It is widely exported agri-produce with global turnover of > 10 billion USD. It is majorly affected by the mosaic or marble disease and hence warrants the deep study at molecular level. Till now, there is no availability of whole genome sequence along with any genomic resources. Under such cases, RNA seq approach can be a rapid and economical alternative to gather the information at genomic level. De novo transcriptome assembly was carried out using Illumina Hiseq data. Analysis revealed a total of 5317 differentially expressed genes, 2267 transcription factors, >100 pathways and 175,952 genic region putative markers. Gene regulatory network analysis was performed to see the molecular events playing role in marble disease. We report the first transcriptomic results that shows the disease mechanism mediated by perturbation in auxin homeostasis and ethylene signaling. These events lead to senescence. We also developed the web-genomic resource, SCMVTDb which houses putative molecular markers, candidate genes and transcript information. Such web resource can be used in small cardamom germplasm improvement against mosaic disease in endeavour of its increased productivity.

scholarly journals Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1086-1088 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O.I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Perennial Ryegrass ◽  
Transcriptome Assembly ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Grass Species ◽  
Rna Seq ◽  
Pasture Grass ◽  
Tissue Samples ◽  
Genome Sequence Assembly ◽  
Transcriptome Resource

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931 547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions.

scholarly journals RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0125722 ◽  
Author(s):  
Yuli Li ◽  
Xiliang Wang ◽  
Tingting Chen ◽  
Fuwen Yao ◽  
Cuiping Li ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Gene Discovery ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Cistanche Deserticola

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

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.

De novo transcriptome assembly and analysis of the codon usage bias of the MADS-box gene family in Cymbidium kanran

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Boyun Yang ◽  
Huolin Luo ◽  
Yuan Tao ◽  
Wenjing Yu ◽  
Liping Luo
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Mads Box ◽  
Illumina Hiseq ◽  
Optimal Codons ◽  
Mads Box Gene ◽  
New Varieties

Cymbidium kanran is an important commercially grown member of the Chinese orchid family. However, little information regarding the molecular biology of this species is available. In this study, the C. kanran root, shoot, stem, leaf, and flower transcriptomes were sequenced with the Illumina HiSeq 4000 system, which resulted in 8.9 Gb of clean reads that were assembled into 74,620 unigenes, with an average length and N50 of 983 bp and 1,640 bp, respectively. The screening of seven databases (NR, NT, GO, KOG, KEGG, Swiss-Prot, and InterPro) for similar sequences resulted in the functional annotation of 49,813 unigenes. Additionally, 173 MADS-box genes, which help to control major aspects of plant development, were identified and their codon usage bias was analyzed. Only 26 genes had a low ENC (less than or equal to 35), suggesting the codon usage bias was weak. Base mutations were the major determinants of codon usage, although natural selection pressure also influenced codon usage bias. Moreover, 22 optimal codons were identified based on ΔRSCU, and 20 codons ended with A/U. The results of this study provide the foundation for the molecular breeding of new varieties

scholarly journals Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 631
Author(s):  
Zhicheng Sun ◽  
Fangrui Lou ◽  
Yuan Zhang ◽  
Na Song
Keyword(s):  
Signal Transduction ◽  
Salinity Stress ◽  
De Novo ◽  
Enrichment Analysis ◽  
Gill Tissue ◽  
Control Group ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Pathways Analysis

Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.

scholarly journals Identification of cordycepin biosynthesis-related genes through de novo transcriptome assembly and analysis in Cordyceps cicadae

2018 ◽  
Vol 5 (12) ◽  
pp. 181247 ◽  
Author(s):  
Tengfei Liu ◽  
Ziyao Liu ◽  
Xueyan Yao ◽  
Ying Huang ◽  
Qingsong Qu ◽  
...  
Keyword(s):  
Fruiting Body ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Quantitative Polymerase Chain Reaction ◽  
Nucleotide Metabolism ◽  
Differentially Expressed ◽  
Parasitic Fungus ◽  
Active Constituent ◽  
Illumina Hiseq ◽  
Cordyceps Cicadae

Cordyceps cicadae (Chanhua) is a parasitic fungus that grows on Cicada flammata larvae and is used to relieve exhaustion and treat numerous diseases, in part through its active constituent, cordycepin. We used de novo Illumina HiSeq 4000 sequencing to obtain transcriptomes of C. cicadae mycelium, fruiting body, and sclerotium, and identify differentially expressed genes. In the mycelium versus sclerotium libraries, 1576 upregulated and 2300 downregulated genes were identified. In the mycelium versus fruiting body and fruiting body versus sclerotium body libraries, 1604 and 1474 upregulated and 1365 and 1320 downregulated genes, respectively, were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified 19 genes differentially expressed in mycelium versus fruiting body as related to the purine pathway, along with 28 and 16 genes differentially expressed in the mycelium versus sclerotium and fruiting body versus sclerotium groups, respectively. Gene expression of six key enzymes was validated by quantitative polymerase chain reaction. Specifically, 5′-nucleotidase (c62060g1) and adenosine deaminase (c35629g1) in purine nucleotide metabolism, which are involved in cordycepin biosynthesis, were significantly upregulated in the sclerotium group. These findings improved our understanding of genes involved in the biosynthesis of cordycepin and other characteristic secondary metabolites in C. cicadae .

scholarly journals De novo transcriptome assembly of RNA-Seq reads with different strategies

2011 ◽  
Vol 54 (12) ◽  
pp. 1129-1133 ◽  
Author(s):  
Geng Chen ◽  
KangPing Yin ◽  
Charles Wang ◽  
TieLiu Shi
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome

scholarly journals rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

2018 ◽  
Author(s):  
Elena Bushmanova ◽  
Dmitry Antipov ◽  
Alla Lapidus ◽  
Andrey D. Prjibelski
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
Challenging Problem ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Weak Points ◽  
Transcriptome Reconstruction ◽  
Evaluation Approaches ◽  
Genome Assembler

AbstractSummaryPossibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.

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