September 22, 2019  |  

Single-molecule long-read sequencing facilitates shrimp transcriptome research.

Authors: Zeng, Digang and Chen, Xiuli and Peng, Jinxia and Yang, Chunling and Peng, Min and Zhu, Weilin and Xie, Daxiang and He, Pingping and Wei, Pinyuan and Lin, Yong and Zhao, Yongzhen and Chen, Xiaohan

Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.

Journal: Scientific reports
DOI: 10.1038/s41598-018-35066-3
Year: 2018

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