Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi office, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.
Biosensing and Bioprospecting Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
BMC Genomics. 2022 Aug 6;23(1):565. doi: 10.1186/s12864-022-08802-3.
Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. Endogenous viral elements (EVE) play a role in this process probably via production of negative-sense Piwi-interacting RNA (piRNA)-like fragments. These bind with Piwi proteins to dampen viral replication via the RNA interference (RNAi) pathway. We searched a genome sequence (GenBank record JABERT000000000) of the giant tiger shrimp (Penaeus monodon for the presence of EVE related to a shrimp parvovirus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV).
The shrimp genome sequence contained three piRNA-like gene clusters containing scrambled IHHNV EVE. Two clusters were located distant from one another in pseudochromosome 35 (PC35). Both PC35 clusters contained multiple sequences with high homology (99%) to GenBank records DQ228358 and EU675312 that were both called "non-infectious IHHNV Type A" (IHHNV-A) when originally discovered. However, our results and those from a recent Australian P. monodon genome assembly indicate that the relevant GenBank records for IHHNV-A are sequence-assembly artifacts derived from scrambled and fragmental IHHNV-EVE. Although the EVE in the two PC35 clusters showed high homology only to IHHNV-A, the clusters were separate and distinct with respect to the arrangement (i.e., order and reading direction) and proportional content of the IHHNV-A GenBank records. We conjecture that these 2 clusters may constitute independent allele-like clusters on a pair of homologous chromosomes. The third EVE cluster was found in pseudochromosome 7 (PC7). It contained EVE with high homology (99%) only to GenBank record AF218266 with the potential to protect shrimp against current types of infectious IHHNV. One disadvantage was that some EVE in PC7 can give false positive PCR test results for infectious IHHNV.
Our results suggested the possibility of viral-type specificity in EVE clusters. Specificity is important because whole EVE clusters for one viral type would be transmitted to offspring as collective hereditary units. This would be advantageous if one or more of the EVE within the cluster were protective against the disease caused by the cognate virus. It would also facilitate gene editing for removal of non-protective EVE clusters or for transfer of protective EVE clusters to genetically improve existing shrimp breeding stocks that might lack them.
虾类具有在长期、持续性感染中容纳病毒而不出现疾病迹象的能力。内源性病毒元件（EVE）可能通过产生负义 Piwi 相互作用 RNA（piRNA）样片段在这一过程中发挥作用。这些片段与 Piwi 蛋白结合，通过 RNA 干扰（RNAi）途径抑制病毒复制。我们在巨型虎虾（Penaeus monodon）的基因组序列（GenBank 记录 JABERT000000000）中搜索了与虾类细小病毒有关的 EVE，该细小病毒最初被命名为传染性皮下和造血坏死病毒（IHHNV）。
虾类基因组序列包含三个 piRNA 样基因簇，其中包含杂乱无章的 IHHNV EVE。两个簇位于假染色体 35（PC35）的彼此远离的位置。两个 PC35 簇都包含多个与 GenBank 记录 DQ228358 和 EU675312 高度同源（99%）的序列，最初发现时这两个记录都被称为“非传染性 IHHNV-A”（IHHNV-A）。然而，我们的结果以及最近澳大利亚 P. monodon 基因组组装的结果表明，GenBank 记录中与 IHHNV-A 相关的记录是源自杂乱无章和碎片化的 IHHNV-EVE 的序列组装伪迹。尽管两个 PC35 簇中的 EVE 仅与 IHHNV-A 高度同源，但这些簇在排列（即顺序和阅读方向）和 IHHNV-A GenBank 记录的比例内容上是独立和不同的。我们推测，这两个簇可能构成同源染色体上一对独立的等位基因样簇。第三个 EVE 簇位于假染色体 7（PC7）中。它包含与 GenBank 记录 AF218266 高度同源（99%）的 EVE，具有保护虾类免受当前类型的传染性 IHHNV 的潜力。一个缺点是，PC7 中的一些 EVE 可能会导致传染性 IHHNV 的 PCR 检测结果出现假阳性。
我们的研究结果表明 EVE 簇可能具有病毒类型特异性。特异性很重要，因为一个病毒类型的整个 EVE 簇将作为集体遗传单位传递给后代。如果簇内的一个或多个 EVE 具有针对相应病毒的保护作用，这将是有利的。它还将促进基因编辑以去除非保护性 EVE 簇，或转移保护性 EVE 簇以遗传改良可能缺乏它们的现有虾类养殖种群。
