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. 2016 Dec 2;7(12):114.
doi: 10.3390/genes7120114.

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

Jiyeon Seong  1 , Se Won Kang  2 , Bharat Bhusan Patnaik  3   4 , So Young Park  5 , Hee Ju Hwang  6 , Jong Min Chung  7 , Dae Kwon Song  8 , Mi Young Noh  9 , Seung-Hwan Park  10 , Gwang Joo Jeon  11 , Hong Sik Kong  12 , Soonok Kim  13 , Ui Wook Hwang  14 , Hong Seog Park  15 , Yeon Soo Han  16 , Yong Seok Lee  17
Affiliations

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

Jiyeon Seong et al. Genes (Basel). .

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.

Keywords: Illumina sequencing; SSRs (simple sequence repeats); Triops longicaudatus; tadpole shrimp; transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Size distribution of contigs (blue) and unigenes (red) after assembly and clustering of the quality reads from the transcriptome of T. longicaudatus.
Figure 2
Figure 2
The sequence annotation profile of T. longicaudatus unigenes against PANM-DB, Unigene DB and KOG DB.
Figure 3
Figure 3
Homology searches of T. longicaudatus unigenes against the PANM-DB. (A) E-value distribution; (B) Top-hit species distribution.
Figure 3
Figure 3
Homology searches of T. longicaudatus unigenes against the PANM-DB. (A) E-value distribution; (B) Top-hit species distribution.
Figure 4
Figure 4
KOG DB based functional analysis of T. longicaudatus unigenes.
Figure 5
Figure 5
GO term classification for T. longicaudatus. (A) Predicted functional interpretation of unigenes into represented biological process, cellular component, and molecular function; (B) Number of unigene sequences annotated with numbers of GO terms per sequence.
Figure 6
Figure 6
GO annotation of unigenes from T. longicaudatus based on biological processes, molecular functions and cellular components.
Figure 7
Figure 7
Identified KEGG pathways of assembled unigenes from T. longicaudatus.
Figure 8
Figure 8
The number of SSRs discovered in the unigenes from T. longicaudatus based on motif sequence types.
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