Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing

Abstract

The dinoflagellate Akashiwo sanguinea is a harmful algal species and commonly observed in estuarine and coastal waters around the world. Harmful algal blooms (HABs) caused by this species lead to serious environmental impacts in the coastal waters of China since 1998 followed by huge economic losses. However, the full-length transcriptome information of A. sanguinea is still not fully explored, which hampers basic genetic and functional studies. Herein, single-molecule real-time (SMRT) sequencing technology was performed to characterize the full-length transcript in A. sanguinea. Totally, 83.03 Gb SMRT sequencing clean reads were generated, 983,960 circular consensus sequences (CCS) with average lengths of 3,061 bp were obtained, and 81.71% (804,016) of CCS were full-length non-chimeric reads (FLNC). Furthermore, 26,461 contigs were obtained after being corrected with Illumina library sequencing, with 20,037 (75.72%) successfully annotated in the five public databases. A total of 13,441 long non-coding RNA (lncRNA) transcripts, 3,137 alternative splicing (AS) events, 514 putative transcription factors (TFs) members from 23 TF families, and 4,397 simple sequence repeats (SSRs) were predicted, respectively. Our findings provided a sizable insights into gene sequence characteristics of A. sanguinea, which can be used as a reference sequence resource for A. sanguinea draft genome annotation, and will contribute to further molecular biology research on this harmful bloom algae.

Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing

“…To obtain more detailed information about the target species transcriptome, the strategy of pooling samples from different treatments or tissues has been frequently performed with SMRT sequencing [ 25 , 28 ]. For instance, three different growth stages and several nutritional culture conditions of the dinoflagellate Akashiwo sanguinea were collected for SMRT sequencing library construction [ 25 ]. For H .…”

“…In recent years, third-generation sequencing (e.g., single-molecule real-time [SMRT]) technologies have been able to address the shortcoming of NGS. Single-molecule real-time sequencing can obtain full-length transcript sequences, without assembly, providing a better opportunity to explore whole-transcriptome profiling in non-model species [ 25 , 26 , 27 , 28 ].…”

Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates

“…Earlier studies of transcriptome data identified: (a) differentially expressed genes in dinoflagellates relative to lifestyle (Bellantuono et al 2019), and to biotic and abiotic stresses (Moustafa et al 2010;Lowe et al 2011;Wang et al 2019;Kang et al 2021), (b) the transsplicing of spliced-leader sequences at the 5′-end of mature mRNAs (Zhang et al 2007), (c) diversity of transcript isoforms (Chen et al 2022a), and, more recently in combination with genome data, (d) protein-coding sequences (Shoguchi et al 2013;Lin et al 2015;Aranda et al 2016;Shoguchi et al 2018;Chen et al 2020;Stephens et al 2020;González-Pech et al 2021;Chen et al 2022b), and (e) the differential editing of mRNAs (Liew et al 2017;Dougan et al 2022b) and differential exon usage (Dougan et al 2022a) in distinct growth conditions. In most cases, these studies employed standard RNA-Seq approaches for eukaryotes to generate transcriptome data, whereby mRNAs with polyadenylated tails are retained, and focused on protein-coding genes.…”