Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing.
Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing.
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通过单分子实时测序对水华形成甲藻 Akashiwo sanguinea 进行全长转录组分析
DOI：
10.3389/fmicb.2022.993914
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发表时间：
2022
影响因子：
5.2
通讯作者：
中科院分区：
文献类型：
--
作者：
血赤藻是一种常见于世界各地河口和沿海沃茨的有害藻类。自1998年以来，该物种在我国沿海沃茨造成了严重的环境影响，并造成了巨大的经济损失。然而，A.血细胞仍然没有得到充分的探索，这阻碍了基本的遗传和功能研究。本文采用单分子实时荧光（SMRT）测序技术对A.血腥共生成83.03 Gb SMRT测序干净读段，获得983，960个平均长度为3，061 bp的环状共有序列（CCS），81.71%（804，016）的CCS为全长非嵌合读段（FLNC）。此外，经Illumina文库测序校正后获得26，461个重叠群，其中20，037个（75.72%）在五个公共数据库中成功注释。共预测了13，441个长非编码RNA（lncRNA）转录本，3，137个选择性剪接（AS）事件，来自23个TF家族的514个推定转录因子（TF）成员，以及4，397个简单序列重复（SSR）。我们的研究结果提供了一个相当大的见解基因序列特征的A。血红蛋白基因可作为A.血红藻基因组草图注释，为进一步开展该赤潮藻的分子生物学研究奠定了基础。
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.
影响因子：
3.7
作者：
Haile S;Corbett RD;LeBlanc VG;Wei L;Pleasance S;Bilobram S;Nip KM;Brown K;Trinh E;Smith J;Trinh DL;Bala M;Chuah E;Coope RJN;Moore RA;Mungall AJ;Mungall KL;Zhao Y;Hirst M;Aparicio S;Birol I;Jones SJM;Marra MA
通讯作者：
Marra MA