Transcriptome analysis of the tadpole shrimp (Triops longicaudatus) by illumina paired-end sequencing: assembly, annotation, and marker discovery

Abstract

The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs. In this study, whole-transcriptome sequencing of T. longicaudatus generated 39.74 GB of clean data and a total of 269,822 contigs using the Illumina HiSeq 2500 platform. After clustering, a total of 208,813 unigenes with an N50 length of 1089 bp were generated. A total of 95,105 unigenes were successfully annotated against Protostome (PANM), Unigene, Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX with a cut-off of 1E-5. A total of 57,731 unigenes were assigned to GO terms, and 7247 unigenes were mapped to 129 KEGG pathways. Furthermore, 1595 simple sequence repeats (SSRs) were detected from the unigenes with 1387 potential SSR markers. This is the first report of high-throughput transcriptome analysis of T. longicaudatus, and it provides valuable insights for genetic research and molecular-assisted breeding of this important species.