De Novo Assembly of Uca minax Transcriptome from Next Generation Sequencing

High-throughput cDNA sequencing (RNA-seq) is a very powerful technique to quantify gene expression in an unbiased way. The Crustacean family is among the groups of organisms sparsely represented in current genomic databases. Here we present transcriptome data from Uca minax (red-jointed fiddler crab...

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Bibliographic Details
Published in:arXiv.org 2020-01
Main Authors: Hanin, Omar, Cole, Casey A, Fahim, Arjang, Gusmaroli, Giuliana, Borgianini, Stephen, Valafar, Homayoun
Format: Article
Language:English
Subjects:
Adapters
Assembly
Crabs
Crustaceans
Freeware
Gene expression
Gene sequencing
Open source software
Quality control
Ribonucleic acid
RNA
Software development tools
Source code
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Summary:High-throughput cDNA sequencing (RNA-seq) is a very powerful technique to quantify gene expression in an unbiased way. The Crustacean family is among the groups of organisms sparsely represented in current genomic databases. Here we present transcriptome data from Uca minax (red-jointed fiddler crab) as an opportunity to extend our knowledge. Next generation sequencing was performed on six tissue samples from Uca minax using the Illumina HiSeq system. Six Transcriptome libraries were created using Trinity; a free, open-source software tool for de novo transcriptome assembly of high-throughput mRNA sequencing (RNA-seq) data with the absence of a reference genome. In addition, several tools that aid in management of data were used, such as RSEM, Bowtie, Blast, and IGV; a tool for visualizing RNA-seq analysis results. Fast quality control (FastQC) analysis of the raw sequenced files revealed that both adapter and PCR primer sequences were prevalently present, which may require a preprocessing step.
ISSN:2331-8422