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 transcriptome assembly for the spiny mouse (Acomys cahirinus)

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Jared Mamrot ◽  
Roxane Legaie ◽  
Stacey J. Ellery ◽  
Trevor Wilson ◽  
Torsten Seemann ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Spiny Mouse ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Acomys Cahirinus

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 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 Siberian sturgeon multi-tissue reference transcriptome database

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Christophe Klopp ◽  
Cédric Cabau ◽  
Gonzalo Greif ◽  
André Lasalle ◽  
Santiago Di Landro ◽  
...  
Keyword(s):  
Reference Genome ◽  
Transcriptome Assembly ◽  
Fish Farming ◽  
Siberian Sturgeon ◽  
Supplementary Information ◽  
Rna Seq ◽  
High Quality ◽  
Reference Transcriptome ◽  
Functional Studies ◽  
Transcriptome Database

Abstract Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets. Availability: The database is publicly available at http://siberiansturgeontissuedb.sigenae.org Supplementary information:  Supplementary data are available at Database online.

scholarly journals High Quality de Novo Transcriptome Assembly of Croton tiglium

2018 ◽  
Vol 5 ◽  
Author(s):  
Markus Haak ◽  
Svenja Vinke ◽  
Willy Keller ◽  
Julian Droste ◽  
Christian Rückert ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
High Quality ◽  
Croton Tiglium

scholarly journals Embryonic gene transcription in the spiny mouse (Acomys cahirinus): an investigtion into the embryonic genome activation

2018 ◽  
Author(s):  
Jared Mamrot ◽  
David K. Gardner ◽  
Peter Temple-Smith ◽  
Hayley Dickinson
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Gene Transcription ◽  
De Novo ◽  
Mouse Embryos ◽  
Spiny Mouse ◽  
Acomys Cahirinus ◽  
Embryonic Genome Activation ◽  
Embryonic Genome ◽  
Genome Activation

Our understanding of genetic mechanisms driving early embryonic development is primarily based on experiments conducted on mice, however translation of findings can be limited by physiological differences between mice and humans. To address this, we investigated whether the spiny mouse (Acomys cahirinus) is a closer model of early human embryonic development due to their more human-like endocrine profile. We therefore characterised the initiation of gene transcription in the spiny mouse embryo and compared the pattern of gene expression during the embryonic genome activation (EGA) with common mouse and human embryos. Naturally-mated spiny mouse embryos were obtained at the 2-cell, 4-cell and 8-cell stages of development (n=4 biological replicates per stage). RNA-Seq of these samples produced 709.1M paired-end reads in total. De novo assembly of reads was conducted using Trinity. Embryo-specific transcripts were extracted from the de novo assembly and added to the reference spiny mouse transcriptome. Transcription was first detected between the 2-cell and 4-cell stages for the majority of genes (n=3,428), with fewer genes first transcribed between the 4-cell and 8-cell stages (n=1,150). The pattern of gene expression in spiny mouse embryos during this period of development is more human-like than common mouse embryos. This is the first evidence the spiny mouse may provide a more suitable model of human embryonic development. The improved reference Acomys cahirinus transcriptome is publically accessible, further increasing the value of this tool for ongoing research. Further investigation into early development in the spiny mouse is warranted.

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 genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens

2020 ◽  
Author(s):  
C. Molitor ◽  
T.J. Kurowski ◽  
P.M. Fidalgo de Almeida ◽  
P. Eerolla ◽  
D.J. Spindlow ◽  
...  
Keyword(s):  
Drought Resistance ◽  
Crop Production ◽  
Reference Genome ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Crop Improvement ◽  
Single Copy ◽  
Analysis Tool ◽  
High Quality ◽  
De Novo Genome Assembly

AbstractSolanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a high-quality reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Here, we present a de novo genome and transcriptome assembly for S. sitiens (Accession LA1974). A hybrid assembly strategy was followed using Illumina short reads (∼159X coverage) and PacBio long reads (∼44X coverage), generating a total of ∼262 Gbp of DNA sequence; in addition, ∼2,670 Gbp of BioNano data was obtained. A reference genome of 1,245 Mbp, arranged in 1,481 scaffolds with a N50 of 1,826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT); this is within the range of current high-quality reference genomes for other tomato wild relatives. Additionally, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7.In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and perform a de novo transcriptome. Some of the protein clusters unique to S. sitiens were associated with genes involved in drought and salt resistance, including GLO1 and FQR1.This first reference genome for S. sitiens will provide a valuable resource to progress QTL studies to the gene level, and will assist molecular breeding to improve crop production in water-limited environments.

scholarly journals Development and validation of microsatellite markers from de novo transcriptome assembly of eggplant (Solanum melongena L.) and its putative progenitor S. incanum L. cultivars

2019 ◽  
Author(s):  
Shailesh K. Tiwari ◽  
Pallavi Mishra ◽  
Sakshi Singh ◽  
Vinay K Singh ◽  
Sarvesh P Kashyap ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Solanum Melongena ◽  
Biotic And Abiotic Stress ◽  
High Quality ◽  
Horticultural Traits ◽  
Parental Lines ◽  
Unique Genes

AbstractAn elite cultivar of eggplant, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.) with contrasting horticultural traits were used as parental lines to develop a mapping population of RILs. To accelerate breeding programs and to develop large scale SSR markers to be used in QTL mapping, RNASeq libraries from different tissues of both the parental plants were deep sequenced and assembled into representation of a high quality de novo transcriptome using Illumina-based Next Generation Sequencing technology. 99.99% of high quality bases were obtained from all the tissues and deposited in TSA database at the NCBI link. Total 3, 156 and 3, 196 SNVs were detected in S. melongena and S. incanum, respectively. In S. melongena, 11, 262 SSR while in S. incanum 11, 829 SSR containing regions were identified. Based on functional annotation, 21, 914 unique genes could be identified for S. melongena, 21,706 unique genes for S. incanum and overall, 60 different transcription factors were identified in both the lines. Further, a total of 536 SSR markers were designed and screened for polymorphism of which, 157 markers produced polymorphism between the parental lines. The polymorphic SSRs shall be used for genotyping of RILs to map QTLs for various horticultural traits in eggplant and identification of candidate genes in response to biotic and abiotic stress.

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