Environment and Regional Development Graduate Program, University of Western São Paulo, Presidente Prudente, São Paulo, Brazil; Biology Department, University of Western São Paulo, Presidente Prudente, São Paulo, Brazil.
Cell Biology, Physiology, and Immunology Department, School of Biology, University of Barcelona, 643 08028 Barcelona, Catalonia, Spain.
Comp Biochem Physiol Part D Genomics Proteomics. 2023 Mar;45:101041. doi: 10.1016/j.cbd.2022.101041. Epub 2022 Nov 22.
Interspecific hybrids are highly complex organisms, especially considering aspects related to the organization of genetic material. The diversity of possibilities created by the genetic combination between different species makes it difficult to establish a large-scale analysis methodology. An example of this complexity is Tambacu, an interspecific hybrid of Colossoma macropomum (Tambaqui) and Piaractus mesopotamicus (Pacu). Either genotype represents an essential role in South American aquaculture. However, despite this importance, the genetic information for these genotypes is still highly scarce in specialized databases. Using RNA-Seq analysis, we characterized the transcriptome of white muscle from Pacu, Tambaqui, and their interspecific hybrid (Tambacu). The sequencing process allowed us to obtain a significant number of reads (approximately 53 billion short reads). A total of annotated contigs were 37,285, 96,738, and 158,709 for Pacu, Tambaqui, and Tambacu. After that, we performed a comparative analysis of the transcriptome of the three genotypes, where we evaluated the differential expression (Tambacu vs Pacu = 11,156, and Tambacu vs Tambaqui = 876) profile of the transcript and the degree of similarity between the nucleotide sequences between the genotypes. We assessed the intensity and pattern of expression across genotypes using differential expression information. Clusterization analysis showed a closer relationship between Tambaqui and Tambacu. Furthermore, digital differential expression analysis selected some target genes related to essential cellular processes to evaluate and validate the expression through the RT-qPCR. The RT-qPCR analysis demonstrated significantly (p < 0.05) elevated expression of the mafbx, foxo1a, and rgcc genes in the hybrid compared to the parents. Likewise, we can observe genes significantly more expressed in Pacu (mtco1 and mylpfa) and mtco2 in Tambaqui. Our results showed that the phenotype presented by Tambacu might be associated with changes in the gene expression profile and not necessarily with an increase in gene variability. Thus, the molecular mechanisms underlying these "hybrid effects" may be related to additive and, in some cases, dominant regulatory interactions between parental alleles that act directly on gene regulation in the hybrid transcripts.
种间杂种是高度复杂的生物体，特别是考虑到与遗传物质组织相关的方面。不同物种之间的遗传组合所产生的多样性使得建立大规模分析方法变得困难。Tambacu 就是一个例子，它是 Colossoma macropomum（Tambaqui）和 Piaractus mesopotamicus（Pacu）的种间杂种。这两种基因型在南美水产养殖中都具有重要作用。然而，尽管如此重要，这些基因型的遗传信息在专门的数据库中仍然非常稀缺。我们使用 RNA-Seq 分析对 Pacu、Tambaqui 和它们的种间杂种（Tambacu）的白肌转录组进行了表征。测序过程使我们获得了大量的读数（大约 530 亿个短读数）。Pacu、Tambaqui 和 Tambacu 的注释连续体总数分别为 37285、96738 和 158709。之后，我们对三种基因型的转录组进行了比较分析，评估了转录物的差异表达（Tambacu vs Pacu=11156，和 Tambacu vs Tambaqui=876）谱和基因型之间核苷酸序列的相似性程度。我们使用差异表达信息评估了跨基因型的表达强度和模式。聚类分析显示 Tambaqui 和 Tambacu 之间的关系更为密切。此外，数字差异表达分析选择了一些与重要细胞过程相关的靶基因，通过 RT-qPCR 进行评估和验证表达。RT-qPCR 分析表明，与亲本相比，杂种中 mafbx、foxo1a 和 rgcc 基因的表达显著（p<0.05）升高。同样，我们可以观察到 Pacu 中表达显著更高的基因（mtco1 和 mylpfa）和 Tambaqui 中的 mtco2。我们的结果表明，Tambacu 表现出的表型可能与基因表达谱的变化有关，而不一定与基因变异的增加有关。因此，这些“杂种效应”背后的分子机制可能与亲本等位基因之间的加性和在某些情况下的显性调控相互作用有关，这些相互作用直接作用于杂种转录物中的基因调控。
