Recently, a third-generation sequencing (TGS) platform was released that produces long but relatively low-quality reads up to 20 kb in length ( Roberts et al., 2013). However, we lack transcriptomic or genomic evidence concerning the molecular mechanisms underlying the RCC-L and GF-L hybrids. Based on the results of previous research comparing their 5S rDNA and simple sequence repeats (SSRs), we found that the GF-L and RCC-L were similar to natural GF and red crucian carp (RCC), respectively. Interestingly, the GF-L has beautiful twin tails. In terms of appearance, significant phenotypic differences were observed between GF-L, RCC-L, and their original parents (koi carp (KOC) and blunt snout bream (BSB)) for example, compared with KOC and BSB, RCC-L and GF-L have unique characteristics such as blue eyes, small heads and transparent bodies. Recently, we successfully obtained homodiploid hybrids of red crucian carp-like (RCC-L) homodiploid fish and goldfish-like (GF-L) homodiploid fish ( Wang et al., 2018) ( Figure 1). However, few reports have focused on homoploid hybrids. Most of the distant hybrid progenies are reported to be allotetraploid, autotetraploid, or allodiploid ( Liu, 2010). Among all vertebrate classes, the distant hybridization of fish has been deliberately conducted between species, genera, subfamilies, and orders ( ). Nevertheless, there is insufficient evidence to support the hypothesis.ĭistant hybridization is defined as interspecific hybridization, i.e., combining whole genomes from two distinct taxa, which may generate offspring with different phenotypes and genotypes ( Biradar and Rayburn, 2016). Generally, people think GF originated from crucian carp. An obvious difference between GF and wild crucian carp is the distinctly split double tail of the GF. GF and wild crucian carp vary in shape and color. However, this hypothesis lacks direct evidence. According to historical records, the GF derived from a wild silver-grey crucian carp that first mutated into a red-yellow gold crucian carp and was then domesticated during several periods ( Watson et al., 1963 Fu and Shisan, 2016 Wang et al., 2018). Some studies suggest that GF evolved from wild crucian carp ( Chen et al., 2015). However, the evolutionary origins of GF remain unknown. Goldfish (GF), which are popular pets among Chinese people, are cyprinid fish and are considered to be variants of crucian carp ( Wang et al., 2014). Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF. The sequences from the genome resequencing of RCC-L and GF-L were mapped to the genome sequences of CC and BSB, revealing that the similarities of both RCC-L and GF-L to the CC genome (92.52%, 90.18%) were obviously higher than to the BSB genome (50.33%, 49.18%), supporting the suggestion that the genomes of both RCC-L and GF-L were mainly inherited from KOC but had some DNA fragments from BSB. In RCC-L and GF-L, 63.70% and 68.20% of the genetic materials were from KOC, and 12.30% and 11.90% of the genetic materials were from BSB. The results showed that 48.20% and 46.50% of the genes were chimaera and that 3.70% and 8.30% of the genes were mutations of orthologous genes in RCC-L and GF-L, respectively. We also mapped the orthologous genes to the common carp (CC) and BSB genomes and classified them into eight gene patterns in three categories (chimaera, mutant, and biparental origin genes). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB.

Here, we investigated the full-length (FL) transcriptomes and the sequences resulting from the genome resequencing of the red crucian carp-like homodiploid fish (RCC-L) and goldfish-like homodiploid fish (GF-L) derived from the interspecific hybridization of koi carp (KOC) and blunt snout bream (BSB) to provide molecular evidence for the hybrid origin of the goldfish (GF). Knowledge of the early stages of post-hybridization evolution is particularly important. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. 2College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Chinaĭistant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities.1State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China.Yude Wang 1,2† Huifang Tan 1† Minghe Zhang 1 Rurong Zhao 1 Shi Wang 1 Qinbo Qin 1 Jing Wang 1 Chun Zhang 1 Min Tao 1 Ming Ma 2 Bo Chen 2 Shaojun Liu 1*

Hybrid ranchu goldfish