scholarly journals De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Mallikarjuna Rao Kovi ◽  
Helga Amdahl ◽  
Muath Alsheikh ◽  
Odd Arne Rognli
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Red Clover ◽  
Seed Setting ◽  
Reference Transcriptome ◽  
Insight Into

scholarly journals De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
J. Fibla ◽  
N. Oromi ◽  
M. Pascual-Pons ◽  
J. L. Royo ◽  
A. Palau ◽  
...  
Keyword(s):  
Differential Expression ◽  
Brown Trout ◽  
Salmo Trutta ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Cdna Libraries ◽  
Significant Differential Expression ◽  
Reference Transcriptome ◽  
Salmonid Species

Abstract Objectives The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of salmonid species. Data description We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

scholarly journals De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 453 ◽  
Author(s):  
Steven A Yates ◽  
Martin T Swain ◽  
Matthew J Hegarty ◽  
Igor Chernukin ◽  
Matthew Lowe ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Gene Discovery ◽  
Red Clover ◽  
Drought Response ◽  
Rna Seq ◽  
Response Gene ◽  
Insight Into ◽  
Marker Identification

scholarly journals Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1)

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247180
Author(s):  
Fu-Jin Wei ◽  
Saneyoshi Ueno ◽  
Tokuko Ujino-Ihara ◽  
Maki Saito ◽  
Yoshihiko Tsumura ◽  
...  
Keyword(s):  
Male Sterility ◽  
Cryptomeria Japonica ◽  
Evolutionary Biology ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Single Copy ◽  
Reference Transcriptome ◽  
Three Stages ◽  
Significant Expression ◽  
Short Timeframe

Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. Compared to other full-length cDNA resources collected by Sanger and PacBio sequencers, the extent of the coverage in our dataset was the highest, indicating that these data can be safely used for further studies. When two tissue-specific libraries were compared, there were significant expression differences between male strobili and leaf and bark sets. Moreover, subtle expression difference between male-fertile and sterile libraries were detected. Orthologous genes from other model plants and conifer species were identified. We demonstrated that our transcriptome assembly output (CJ3006NRE) can serve as a reference transcriptome for future functional genomics and evolutionary biology studies.

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

scholarly journals RNA-Seq of the Caribbean reef-building coralOrbicella faveolata(Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1616 ◽  
Author(s):  
David A. Anderson ◽  
Marcus E. Walz ◽  
Ernesto Weil ◽  
Peter Tonellato ◽  
Matthew C. Smith
Keyword(s):  
Innate Immunity ◽  
Immune System ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Coral Disease ◽  
Thermal Anomaly ◽  
Molecular Physiology ◽  
Reference Transcriptome ◽  
Caribbean Reef ◽  
The Caribbean

Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease. The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral,Orbicella faveolata. Samples were collected during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463O. faveolatatranscripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. Results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling.O. faveolatais a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.

scholarly journals De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 521 ◽  
Author(s):  
Dylan Richards ◽  
Ludivine Renaud ◽  
Nisha Agarwal ◽  
E. Starr Hazard ◽  
John Hyde ◽  
...  
Keyword(s):  
Algal Blooms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Comparative Genomic ◽  
Sequence Information ◽  
Assembly Technology ◽  
Sardinops Sagax ◽  
Insight Into ◽  
Pleuronichthys Verticalis

The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).

scholarly journals De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

2016 ◽  
Author(s):  
Jared Mamrot ◽  
Roxane Legaie ◽  
Stacey J Ellery ◽  
Trevor Wilson ◽  
David K. Gardner ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Mammalian Species ◽  
Physiological Characteristics ◽  
Spiny Mouse ◽  
High Quality ◽  
Acomys Cahirinus ◽  
Reference Transcriptome ◽  
Spiny Mice ◽  
Mouse Transcriptome

AbstractBackground: Spiny mice of the genus Acomys are small desert-dwelling rodents that display physiological characteristics not typically found in rodents. Recent investigations have reported a menstrual cycle and scar free-wound healing in this species; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique physiological traits, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research. However, little genetic information is currently available for Acomys, limiting the application of some modern investigative techniques. This project aimed to generate a reference transcriptome assembly for the common spiny mouse (Acomys cahirinus).Results: Illumina RNA sequencing of male and female spiny mice produced 451 million, 150bp paired-end reads from 15 organ types. An extensive survey of de novo transcriptome assembly approaches of high-quality reads using Trinity, SOAPdenovo-Trans, and Velvet/Oases at multiple kmer lengths was conducted with 49 single-kmer assemblies generated from this dataset, with and without in silico normalization and probabilistic error correction. Merging transcripts from 49 individual single-kmer assemblies into a single meta-assembly of non-redundant transcripts using the EvidentialGene ‘tr2aacds’ pipeline produced the highest quality transcriptome assembly, comprised of 880,080 contigs, of which 189,925 transcripts were annotated using the SwissProt/Uniprot database.Conclusions: This study provides the first detailed characterization of the spiny mouse transcriptome. It validates the application of the EvidentialGene ‘tr2aacds’ pipeline to generate a high-quality reference transcriptome assembly in a mammalian species, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.

scholarly journals De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1017
Author(s):  
Mohammed Bakkali ◽  
Rubén Martín-Blázquez ◽  
Mercedes Ruiz-Estévez ◽  
Manuel A. Garrido-Ramos
Keyword(s):  
Functional Annotation ◽  
Vascular Plants ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Systematic Position ◽  
Important Data ◽  
Ecological Requirements ◽  
Physiological Adaptations ◽  
Fern Species ◽  
Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

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