A Pipeline for Non-model Organisms for de novo Transcriptome Assembly, Annotation, and Gene Ontology Analysis Using Open Tools: Case Study with Scots Pine

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

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A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

BMC Genomics ◽

10.1186/s12864-017-3735-1 ◽

2017 ◽

Vol 18 (S4) ◽

Cited By ~ 5

Author(s):

Sing-Hoi Sze ◽

Meaghan L. Pimsler ◽

Jeffery K. Tomberlin ◽

Corbin D. Jones ◽

Aaron M. Tarone

Keyword(s):

Efficient Algorithm ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Memory Efficient

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

Planta Medica ◽

10.1055/a-0630-5925 ◽

2018 ◽

Vol 84 (12/13) ◽

pp. 920-934 ◽

Cited By ~ 10

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.

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Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study

High-Throughput ◽

10.3390/ht8040020 ◽

2019 ◽

Vol 8 (4) ◽

pp. 20

Author(s):

Carlos Caicedo-Montoya ◽

Laura Pinilla ◽

León F. Toro ◽

Jeferyd Yepes-García ◽

Rigoberto Ríos-Estepa

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Streptomyces Clavuligerus ◽

Differentially Expressed ◽

Software Performance ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Transcript Quantification

The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms.

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Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

BMC Bioinformatics ◽

10.1186/1471-2105-13-170 ◽

2012 ◽

Vol 13 (1) ◽

pp. 170 ◽

Cited By ~ 24

Author(s):

Berat Z Haznedaroglu ◽

Darryl Reeves ◽

Hamid Rismani-Yazdi ◽

Jordan Peccia

Keyword(s):

High Throughput ◽

Functional Annotation ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

Sequencing Data ◽

De Novo Transcriptome ◽

Short Read ◽

Short Read Sequencing

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The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

PeerJ ◽

10.7717/peerj.5428 ◽

2018 ◽

Vol 6 ◽

pp. e5428 ◽

Cited By ~ 22

Author(s):

Matthew D. MacManes

Keyword(s):

High Throughput Sequencing ◽

Population Genomics ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Biological Phenomena ◽

Complicated Process ◽

Downstream Analysis

Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary, and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at https://github.com/macmanes-lab/Oyster_River_Protocol. Instructions for software installation and use, and other details are available at http://oyster-river-protocol.rtfd.org/.

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Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys)

Data in Brief ◽

10.1016/j.dib.2021.107267 ◽

2021 ◽

pp. 107267

Author(s):

Michael G.C. Brown ◽

Jeff Bowman ◽

Paul J. Wilson

Keyword(s):

North American ◽

De Novo ◽

Transcriptome Assembly ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Flying Squirrels

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Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic

International Journal of Molecular Sciences ◽

10.3390/ijms22136674 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6674

Author(s):

Luisa Albarano ◽

Valerio Zupo ◽

Davide Caramiello ◽

Maria Toscanesi ◽

Marco Trifuoggi ◽

...

Keyword(s):

De Novo ◽

Sea Urchins ◽

Transcriptome Assembly ◽

Paracentrotus Lividus ◽

Marine Biota ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Limit Values ◽

The Impact ◽

Endpoint Approach

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

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