The Single-molecule long-read sequencing of Scylla paramamosain

Abstract

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S . paramamosain , which will greatly facilitate S . paramamosain research.

Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain

“…In our findings, a total of 22,313 lncRNAs were characterized. Interestingly, the number of lncRNAs was similar to the recent report of fulllength transcriptome sequencing for S. paramamosain (Wan et al, 2019), but less remarkably than previous research on lncRNAs from the gonad transcriptome using RNA-Seq (Yang et al, 2018).…”

“…Although SMRT sequencing has been widely used to generate full-length transcriptome in crustaceans (Zeng et al, 2018; Lin et al, 2019;Wan et al, 2019), little full-length transcriptome resources are available for gonads of mud crab. In this study, unique isoform sequences were obtained from the gonad transcriptome by using single molecular long-read sequencing with the PacBio Sequel platform.…”

“…In this study, unique isoform sequences were obtained from the gonad transcriptome by using single molecular long-read sequencing with the PacBio Sequel platform. The high annotation rate of transcripts indicated several advantages of SMRT sequencing over RNA-Seq (Zeng et al, 2018;Wan et al, 2019). Additionally, we identified fusion transcripts based on alignment to gene model annotation; prediction of coding potential is needed to be conducted, and the function of fusion transcripts should be analyzed in a further study.…”

A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean

“…Three libraries with insert sizes of 0.5–6 kb were compared with SMRTbell template prep kits and sequenced on the PacBio Sequel platform. PacBio transcriptome data processing was performed according to Wan et al (2019) with smrt link 6.0 (default mode) (Gordon et al, 2015) and Cdhit V4.7 (99% identity) (Li & Godzik, 2006). Illumina RNA‐seq data were obtained by sequencing 11 libraries generated from samples including a mixture of thoracic and cerebral ganglia, three mandibular organ samples from female crabs, fifth zoea, four megalopa samples, the first juvenile crab stage and copulatory organs from adult male crabs.…”

The Single-Molecule Long-Read Sequencing of Intestine After Soy Meal-Induced Enteritis in Juvenile Pearl Gentian Grouper, Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂

“…Fulllength transcripts can greatly improve the basic and applied research on gene function, gene expression regulation, and the evolutionary relationships of these species (Ren et al, 2006). Previously, obtainment of a full-length gene on a large scale is almost impossible, which is also time-consuming and expensive through RACE and Illumina technology in general (Wan et al, 2019). Currently, most of the transcriptome data are obtained based on next-generation sequencing technologies, such as Illumine, Heliscope, Roche 454, Solexa, and SOLID (Lobato et al, 2017).…”