Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
Fish Shellfish Immunol. 2020 Apr;99:403-413. doi: 10.1016/j.fsi.2020.02.030. Epub 2020 Feb 17.
Siamese fighting fish (Betta splendens) is one of the most widely cultivated ornamental fish in global trade. However, transcriptomic data, which can reveal valuable genetic data for disease control and prevention, are extremely limited for this species. In this study, whole-body transcriptome sequencing of juvenile betta fish generated 4.457 GB of clean data and a total of 71,775 unigenes using the Illumina HiSeq4000 platform. These unigenes were functionally classified using 7 functional databases, yielding 45,316 NR (63.14%), 47,287 NT (65.88%), 39,105 Swiss-Prot (54.48%), 16,492 COG (22.98%), 37,694 KEGG (52.52%), 4,506 GO (6.28%), and 35,374 Interpro (49.28%) annotated unigenes. Furthermore, we also detected 13,834 SSRs distributed on 10,636 unigenes and 49,589 predicted CDSs. Based on KEGG analysis, five innate immune pathways (997 unigenes) were reported, including the NOD-like receptor signaling pathway, complement and coagulation cascades, toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and cytosolic DNA-sensing pathway. Moreover, four antimicrobial peptide (AMP) families (hepcidin, piscidin, LEAP-2, and defensins) from the betta fish transcriptome were also identified. Additionally, cDNA and genomic DNA of two β-defensins was successfully isolated from four betta fish species. RT-PCR analysis showed that BsBD1 transcripts were most abundant in the muscle and kidney and BsBD2 transcripts were most abundant in the gill. The genomic organization showed that the BD1 and BD2 genes consisted of three exons and two introns according to the GT-AG rule. Most importantly, this is the first report of the betta fish whole-body transcriptome obtained by high-throughput sequencing. Our transcriptomic data and the discovery of betta fish AMPs should promote a better understanding of molecular immunology for disease prevention for further ornamental fish aquaculture.
暹罗斗鱼（Betta splendens）是全球贸易中最广泛养殖的观赏鱼类之一。然而，对于这种鱼类，转录组数据（可以揭示疾病控制和预防的有价值的遗传数据）极其有限。在这项研究中，使用 Illumina HiSeq4000 平台对幼年斗鱼进行了全基因组转录组测序，生成了 4.457GB 的清洁数据和总共 71775 个非冗余基因。这些非冗余基因使用 7 个功能数据库进行功能分类，产生了 45316NR（63.14%）、47287NT（65.88%）、39105Swiss-Prot（54.48%）、16492COG（22.98%）、37694KEGG（52.52%）、4506GO（6.28%）和 35374Interpro（49.28%）注释的非冗余基因。此外，我们还检测到分布在 10636 个非冗余基因和 49589 个预测 CDS 上的 13834 个 SSRs。基于 KEGG 分析，报告了 5 条先天免疫途径（997 个非冗余基因），包括 NOD 样受体信号通路、补体和凝血级联、 Toll 样受体信号通路、RIG-I 样受体信号通路和细胞质 DNA 感应通路。此外，还从斗鱼转录组中鉴定了 4 种抗菌肽（AMP）家族（hepcidin、piscidin、LEAP-2 和 defensins）。此外，还成功从 4 种斗鱼物种中分离出两种β-防御素的 cDNA 和基因组 DNA。RT-PCR 分析显示，BsBD1 转录本在肌肉和肾脏中最丰富，BsBD2 转录本在鳃中最丰富。基因组组织表明，BD1 和 BD2 基因根据 GT-AG 规则由三个外显子和两个内含子组成。最重要的是，这是首次通过高通量测序获得的斗鱼全基因组转录组报告。我们的转录组数据和斗鱼 AMP 的发现应该促进对疾病预防的分子免疫学的更好理解，从而进一步促进观赏鱼养殖。
