scholarly journals De Novo Transcriptome Assembly for Venom Gland in Two Spe-Cies of Spiders (Sinopoda Pengi and Trichonephila Clavata)

2021 ◽  
Author(s):  
Li jun Ding ◽  
Xiu mei Wu ◽  
Cheng gui Zhang ◽  
Peng fei Gao ◽  
Yan Zhang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Functional Characterization ◽  
Venom Gland ◽  
Cdna Libraries ◽  
Predator Prey ◽  
Assembly Result ◽  
Agricultural Use ◽  
The Trinity

Abstract Natural molecules from spider venom are considered potential drugs for diseases including cancer and pain, as well as the development of new biological insecticides for agricultural use. During coevolution in the long-term predator-prey game, spiders have formed a huge molecular diversity of toxins. As of March 1 of 2021, a total of 49,243 spider species had been described, but studies of venom have been performed in only a few hundred of these species due to the difficulty of collecting venom. Two technologies have helped partially dealing with this limitation in the recent past: the screening of cDNA libraries constructed from venom gland mRNAs and the heterologous expression of the coded peptides for functional characterization. In this study, transcriptomic analysis was performed to describe the predicted toxins of Sinopoda pengi (hereafter S. pengi) and Trichonephila clavata (hereafter T. clavata). The Trinity assembly result in 163,418 transcripts, 114,127 unigene of S. pengi and 125,099 transcripts, 87,084 unigene of T. clavata. A total of 22 and 24 unigenes were identified which were predicted to inhibitor cysteine knot (ICK) toxins from S. pengi and T. clavata, respectively. In summary, molecular templates with potential application value in medical and biological fields were obtained by classifying and characterizing presumed venom components, which lays a foundation for the further study of venom.

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 Transcriptome Assembly of Myllocerinus aurolineatus Voss in Tea Plants

2021 ◽  
Vol 5 ◽  
Author(s):  
Xin Xie ◽  
Junmei Jiang ◽  
Meiqing Chen ◽  
Maoxi Huang ◽  
Linhong Jin ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Single Nucleotide ◽  
Functional Studies ◽  
Myllocerinus Aurolineatus ◽  
Tea Plants ◽  
The Trinity ◽  
Simple Sequence

Myllocerinus aurolineatus Voss is a species of the insecta class in the arthropod. In this study, we first observed and identified M. aurolineatus Voss in tea plants in Guizhou, China, where it caused severe quantity and quality losses in tea plants. Knowledge on M. aurolineatus Voss genome is inadequate, especially for biological or functional research. We performed the first transcriptome sequencing by using the Illumina Hiseq™ technique on M. aurolineatus Voss. Over 55.9 million high-quality paired-end reads were generated and assembled into 69,439 unigenes using the Trinity short read software, resulting in a cluster of 1,207 bp of the N50 length. A total of 69,439 genes were predicted by BLAST to known proteins in the NCBI database and were distributed into Gene Ontology (20,190), eukaryotic complete genomes (12,488), and the Kyoto Encyclopedia of Genes and Genomes (3,170). We also identified 96,790 single-nucleotide polymorphisms and 13,121 simple sequence repeats in these unigenes. Our transcriptome data provide a useful resource for future functional studies of M. aurolineatus Voss for dispersal control in tea plants.

scholarly journals De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Tinashe G. Chabikwa ◽  
Francois F. Barbier ◽  
Milos Tanurdzic ◽  
Christine A. Beveridge
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Mangifera Indica ◽  
Rna Extraction ◽  
Gene Discovery ◽  
Persea Americana ◽  
Cdna Libraries ◽  
Local Alignment ◽  
Redundancy Reduction ◽  
Search Tool

AbstractAvocado (Persea americana Mill.), macadamia (Macadamia integrifolia L.) and mango (Mangifera indica L.) are important subtropical tree species grown for their edible fruits and nuts. Despite their commercial and nutritional importance, the genomic information for these species is largely lacking. Here we report the generation of avocado, macadamia and mango transcriptome assemblies from pooled leaf, stem, bud, root, floral and fruit/nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets from which we assembled 63420, 78871 and 82198 unigenes of avocado, macadamia and mango, respectively using a combination of de novo transcriptome assembly and redundancy reduction. These unigenes were functionally annotated using Basic Local Alignment Search Tool (BLAST) to query the Universal Protein Resource Knowledgebase (UniProtKB). A workflow encompassing RNA extraction, library preparation, transcriptome assembly, redundancy reduction, assembly validation and annotation is provided. This study provides avocado, macadamia and mango transcriptome and annotation data, which is valuable for gene discovery and gene expression profiling experiments as well as ongoing and future genome annotation and marker development applications.

scholarly journals Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera

2020 ◽  
Vol 10 (10) ◽  
pp. 3843-3857
Author(s):  
Kira A. Treibergs ◽  
Gonzalo Giribet
Keyword(s):  
Gene Expression ◽  
Division Of Labor ◽  
Differential Gene Expression ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Cdna Libraries ◽  
Living Species ◽  
Differential Gene

Bryozoans are a diverse phylum of marine and freshwater colonial invertebrates containing approximately 6,300 described living species. Bryozoans grow by budding new physiologically connected colony members (zooids) from a founding individual that forms from a metamorphosed larva. In some species these zooids come in different shapes and sizes and are specialized to serve different tasks within the colony. A complex interaction of genotype, environment, and developmental pathway shapes zooid fate, however, the specific mechanisms underlying the establishment of this division of labor remain unknown. Here, the first characterization of differential gene expression between polymorphic zooids of a bryozoan colony is presented. The development of different zooid types of lab-cultured Bugulina stolonifera colonies including feeding autozooids, avicularia (derived non-feeding zooids that are homologous to feeding autozooids but shaped like a bird’s beak), and rhizoids (a branching network of non-feeding anchoring zooids) was explored using RNA sequencing, de novo transcriptome assembly, and differential gene expression analyses. High throughput sequencing of cDNA libraries yielded an average of 14.9 ± 1.3 (SE) million high-quality paired-end reads per sample. Data for the first de novo transcriptome assemblies of B. stolonifera and the first characterization of genes involved in the formation and maintenance of zooid types within a bryozoan colony are presented. In a comparison between autozooid and avicularium tissues, 1,097 significant differentially expressed genes were uncovered. This work provides a much-needed foundation for understanding the mechanisms involved in the development of polymorphic zooids and the establishment of division of labor in bryozoans.

De Novo Transcriptome Assembly and Characterization of Lithospermum officinale to Discover Putative Genes Involved in Specialized Metabolites Biosynthesis

Planta Medica ◽  
2018 ◽  
Vol 84 (12/13) ◽  
pp. 920-934 ◽  
Author(s):  
Amit Rai ◽  
Taiki Nakaya ◽  
Yohei Shimizu ◽  
Megha Rai ◽  
Michimi Nakamura ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Expression Analysis ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Functional Characterization ◽  
Bioactive Metabolites ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Metabolome Analysis ◽  
Lithospermum Officinale

Abstract Lithospermum officinale is a valuable source of bioactive metabolites with medicinal and industrial values. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. This study presents the first effort to establish and characterize de novo transcriptome assembly resource for L. officinale and expression analysis for three of its tissues, namely leaf, stem, and root. Using over 4Gbps of RNA-sequencing datasets, we obtained de novo transcriptome assembly of L. officinale, consisting of 77,047 unigenes with assembly N50 value as 1524 bps. Based on transcriptome annotation and functional classification, 52,766 unigenes were assigned with putative genes functions, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG pathway and gene ontology enrichment analysis using highly expressed unigenes across three tissues and targeted metabolome analysis showed active secondary metabolic processes enriched specifically in the root of L. officinale. Using co-expression analysis, we also identified 20 and 48 unigenes representing different enzymes of lithospermic/chlorogenic acid and shikonin biosynthesis pathways, respectively. We further identified 15 candidate unigenes annotated as cytochrome P450 with the highest expression in the root of L. officinale as novel genes with a role in key biochemical reactions toward shikonin biosynthesis. Thus, through this study, we not only generated a high-quality genomic resource for L. officinale but also propose candidate genes to be involved in shikonin biosynthesis pathways for further functional characterization.

scholarly journals Transcriptome Analysis of Amyloodinium ocellatum Tomonts Revealed Basic Information on the Major Potential Virulence Factors

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1252
Author(s):  
Omkar Byadgi ◽  
Fabio Marroni ◽  
Ron Dirks ◽  
Michela Massimo ◽  
Donatella Volpatti ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Dicentrarchus Labrax ◽  
Molecular Data ◽  
Cdna Libraries ◽  
Reference Database ◽  
Rab Proteins ◽  
Lack Of Information ◽  
Casein Kinases ◽  
Amyloodinium Ocellatum

The ectoparasite protozoan Amyloodinium ocellatum (AO) is the etiological agent of amyloodiniosis in European seabass (Dicentrarchus labrax) (ESB). There is a lack of information about basic molecular data on AO biology and its interaction with the host. Therefore, de novo transcriptome sequencing of AO tomonts was performed. AO trophonts were detached from infested ESB gills, and quickly becoming early tomonts were purified by Percoll® density gradient. Tomont total RNA was processed and quality was assessed immediately. cDNA libraries were constructed using TruSeq® Stranded mRNA kit and sequenced using Illumina sequencer. CLC assembly was used to generate the Transcriptome assembly of AO tomonts. Out of 48,188 contigs, 56.12% belong to dinophyceae wherein Symbiodinium microadriaticum had 94.61% similarity among dinophyceae. Functional annotations of contigs indicated that 12,677 had associated GO term, 9005 with KEGG term. The contigs belonging to dinophyceae resulted in the detection of several peptidases. A BLAST search for known virulent factors from the virulence database resulted in hits to Rab proteins, AP120, Ribosomal phosphoprotein, Heat-shock protein70, Casein kinases, Plasmepsin IV, and Brucipain. Hsp70 and casein kinase II alpha were characterized in-silico. Altogether, these results provide a reference database in understanding AO molecular biology, aiding to the development of novel diagnostics and future vaccines.

scholarly journals ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

2019 ◽  
Author(s):  
Angel Ruiz-Reche ◽  
Joel A. Indi ◽  
Ivan de la Rubia ◽  
Eduardo Eyras
Keyword(s):  
De Novo ◽  
Functional Characterization ◽  
Cost Effective ◽  
Error Rates ◽  
Cdna Libraries ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Long Reads ◽  
A Genome ◽  
Long Read

Long-read sequencing technologies allow the systematic interrogation of transcriptomes from any species. However, functional characterization requires the determination of the correct 5’-to-3’ orientation of reads. Oxford Nanopore Technologies (ONT) allows the direct measurement of RNA molecules in the native orientation (Garalde et al. 2018), but sequencing of complementary-DNA (cDNA) libraries yields generally a larger number of reads (Workman et al. 2018). Although strand-specific adapters can be used, error rates hinder their detection. Current methods rely on the comparison to a genome or transcriptome reference (Wyman and Mortazavi 2018; Workman et al. 2018) or on the use of additional technologies (Fu et al. 2018), which limits the applicability of rapid and cost-effective long-read sequencing for transcriptomics beyond model species. To facilitate the interrogation of transcriptomes de-novo in species or samples for which a genome or transcriptome reference is not available, we have developed ReorientExpress (https://github.com/comprna/reorientexpress), a new tool to perform reference-free orientation of ONT reads from a cDNA library, with our without stranded adapters. ReorientExpress uses a deep neural network (DNN) to predict the orientation of cDNA long-reads independently of adapters and without using a reference.

scholarly journals Integrate Heterogeneous NGS and TGS Data to Boost Genome-free Transcriptome Research

2020 ◽  
Author(s):  
Yangmei Qin ◽  
Zhe Lin ◽  
Dan Shi ◽  
Mindong Zhong ◽  
Te An ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Computational Method ◽  
Protein Coding ◽  
Third Generation Sequencing ◽  
A Genome ◽  
Amphioxus Genome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractIt is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Via integrating ten next generation sequencing (NGS) transcriptome datasets and one third-generation sequencing (TGS) dataset, we built a sequence library of non-redundant expressed transcripts for the amphioxus. The library consisted of overall 91,915 distinct transcripts, 51,549 protein-coding transcripts, and 16,923 novel extragenic transcripts. This substantially improved current amphioxus genome annotation by expanding the distinct gene number from 21,954 to 38,777. We consolidated the library significantly outperformed the genome, as well as de novo method, in transcriptome assembly from multiple aspects. For convenience, we curated the Integrative Transcript Library database of the amphioxus (http://www.bio-add.org/InTrans/). In summary, this work provides a practical solution for most organisms to alleviate the heavy dependence on good quality genome in transcriptome research. It also ensures the amphioxus transcriptome research grounding on reliable data.

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