Using PacBio Iso-Seq to determine the transcriptome of Rhynchophorus ferrugineus
Author of the article:YANG Hong-Jun HU Jia-Meng WANG Zhi-Bo XU Dan-Ping ZHUO Zhi-Hang
Author's Workplace：College of Life Science, China West Normal University, Nanchong 637002, China; College of Forestry, Hainan University, Haikou 570228, China; The Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, P. R. China, Guangzhou 510642, China
Key Words：Rhynchophorus ferrugineus; transcriptome; genome annotation; high-throughput sequencing
Abstract：
[Objectives] To obtain genetic data on, and establish a transcriptome database for, Rhynchophorus ferrugineus. [Methods] The transcriptome of R. ferrugineus was sequenced using a high-throughput sequencing platform with second-generation sequencing (Illumina RNA-seq) to correct third-generation sequencing (PacBio Iso-Seq) data, and analyzed with bioinformatic software. [Results] The mean number of R. ferrugineus transcripts was 2 302 bp and the N90 and N50 lengths were 1 321 bp and 2 785 bp, respectively. An additional 63 801 transcripts were obtained using the CD-Hit program with the majority ranging in length between 0.5 and 6 k. Of the transcripts found, 50 280 were annotated in the NR database, 27 253 in the NT database, 47 197 in the KEGG database, 40 109 in the Swiss-Prot database, 27 707 in the Pfam database, 27 707 in the GO database and 33 511 in the KOG database. 54 999 were annotated in at least one database and 12 058 were annotated in all databases. Furthermore, 2 184 AS, 66 230 SSR, 20 84 TFs and 9 618 LncRNA were predicted, or identified, respectively, and the main CDS length range was 0-2 500 nt. [Concusion] The transcriptome database of R. ferrugineus was successfully obtained. The results provide a foundation for further study of the molecular biology of this species.