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.

The transcriptome of the marine calanoid copepod Temora longicornis under heat stress and recovery

“…Another way to assess the quality of the Temora longicornis transcriptome is to perform a reference-based alignment using BUSCO. The BUSCO results were compared against the arthropod transcriptome reference scores provided in the BUSCO supplementary materials and several recently published crustacean transcriptomes (Figure 6) (Northcutt et al, 2016, Seong et al, 2016, Theissinger et al, 2016Waiho et al, 2017). Our results are comparable with other recent crustacean transcriptomes such as those of Homarus americanus and Cancer borealis, but are lower compared to other copepod transcriptomes, of which BUSCO results are known (Figure 6).…”

Single-molecule long-read sequencing facilitates shrimp transcriptome research

“…Short-read sequencing (Illumina or 454) has been used to produce transcriptomes of some shrimp species, including L. vannamei 17 , 18 , 33 – 40 , Fenneropenaeus merguiensis 41 , 42 , Macrobrachium rosenbergii 43 , Triops newberryi 44 , T. longicaudatus 45 , Pandalus latirostris 46 , Fenneropenaeus chinensis 47 , Palaemon serratus 48 , and Penaeus monodon 49 . The average lengths of transcripts obtained in these studies were ~306–1,027 bp.…”

De Novo RNA Sequencing and Transcriptome Analysis of Monascus purpureus and Analysis of Key Genes Involved in Monacolin K Biosynthesis

“…After this quality control step, 60,348,338 high-quality reads with a length of 101 bp (average length: 86.62bp) were retained (Fig 1): these were used to assemble contigs and obtain transcripts in default parameter settings by the Trinity program [44]. In total, 41,002 contigs were generated with a k-mer of 25, which was pre-defined to avoid misassembly caused by a too-short k-mer while retaining a reasonable number of reads [45,46]. In the step of assembling, 41,002 transcripts had a median size (N50) of 900 bp and 29,713 unigenes had an N50 of 789 bp from all of the contigs; 39% of the unigenes were not shorter than 500 bp and approximately 200 (0.80%) were longer than 2 kb.…”