Full-length transcriptome reveals rapid genetic changes in triploid hybrid grass carp derived from female grass carp × male topmouth culter

Abstract

Distant hybridization refers to the combination of different genomes from different species and further leads to genetic structure changes in hybrids. For next-generation sequencing limitations, the genetic changes with respect to hybrids or polyploids cannot be fully explained. Here, we obtained 117,526 full-length isoforms from a triploid hybrid grass carp (3nGT, 3n = 72) by the crossing of female grass carp (GC, 2n = 48) and male topmouth culter (TC, 2n = 48) using single-molecule long reads sequencing technology. Further, the gene fusion, alternative splicing (AS), transcription of homologous genes, and novel genes were analyzed. The results showed that 1563 fusion genes were detected in 3nGT including 872 heterogenous fusion genes derived from GC and TC genomes. Meanwhile, 175,644 AS events were identified and divided into five models, of which IntronR was the dominant model. In addition, 8964 novel genes were discovered, of which 2802 novel genes were annotated. Finally, scans results of Hox gene family revealed that both GC and TC Hox genes were transcribed in 3nGT, but presented asymmetric transcription patterns with a bias towards the maternal parent GC genome. This study not only provides a rich resource of transcript isoforms for the superior triploid grass carp, but also provides an important insight into rapid genetic changes in hybrid fish.