Transcriptome analysis identifies immune-related genes and antimicrobial peptides in Siamese fighting fish (Betta splendens)
Transcriptome analysis identifies immune-related genes and antimicrobial peptides in Siamese fighting fish (Betta splendens)
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DOI：
10.1016/j.fsi.2020.02.030
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发表时间：
2020-04-01
影响因子：
4.7
通讯作者：
Imjongjirak, Chanprapa
中科院分区：
文献类型：
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作者：
Amparyup, Piti;Charoensapsri, Walaiporn;Imjongjirak, Chanprapa
暹罗斗鱼（β splendens）是全球贸易中最广泛养殖的观赏鱼之一。然而，可以揭示疾病控制和预防有价值的遗传数据的转录组学数据对该物种极为有限。在本研究中，利用Illumina HiSeq4000平台，对幼鱼进行了全身转录组测序，产生了4.457 GB的干净数据，共计71775个单基因。使用7个功能数据库对这些unique进行功能分类，得到45,316个NR(63.14%), 47,287个NT(65.88%), 39,105个Swiss-Prot(54.48%), 16,492个COG(22.98%), 37,694个KEGG(52.52%), 4,506个GO（6.28%）和35,374个Interpro（49.28%）注释unique。此外，我们还检测到分布在10,636个unigenes上的13,834个SSRs和49,589个预测cds。基于KEGG分析，共报道了5条天然免疫通路（997个unique - igenes），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传感通路。此外，还鉴定了4个抗菌肽（AMP）家族（hepcidin、piscidin、LEAP-2和防御素）。此外，还成功地从4种β -防御素中分离出了两种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。基因组组织显示，BD1和BD2基因由3个外显子和2个内含子组成，符合GT-AG规则。最重要的是，这是首次报道通过高通量测序获得的beta鱼全身转录组。我们的转录组学数据和对斗鱼AMPs的发现将促进对分子免疫学的更好理解，为进一步的观赏鱼养殖提供疾病预防。
Siamese fighting fish (Beta 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, tolllike 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 beta-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.