Wang Yude, Tan Huifang, Zhang Minghe, Zhao Rurong, Wang Shi, Qin Qinbo, Wang Jing, Zhang Chun, Tao Min, Ma Ming, Chen Bo, Liu Shaojun
State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China.
College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.
Front Genet. 2020 Mar 3;11:122. doi: 10.3389/fgene.2020.00122. eCollection 2020.
Distant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. Knowledge of the early stages of post-hybridization evolution is particularly important. 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). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB. 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). 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. 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 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. Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF.
远缘杂交导致基因型和表型发生明显变化，产生具有新能力的物种。然而，不同基因组的融合也会聚合在进化过程中发生的DNA或基因变异。了解杂交后进化的早期阶段尤为重要。在此，我们研究了源自锦鲤（KOC）和团头鲂（BSB）种间杂交的红鲫样同源二倍体鱼（RCC-L）和金鱼样同源二倍体鱼（GF-L）的全长（FL）转录组以及基因组重测序产生的序列，为金鱼（GF）的杂交起源提供分子证据。我们将RCC-L和GF-L转录组中的直系同源基因与KOC和BSB的直系同源基因进行了比较。我们还将直系同源基因定位到鲤鱼（CC）和BSB基因组上，并将它们分为三类（嵌合体、突变体和双亲起源基因）中的八种基因模式。结果表明，RCC-L和GF-L中分别有48.20%和46.50%的基因是嵌合体，分别有3.70%和8.30%的基因是直系同源基因的突变。在RCC-L和GF-L中，63.70%和68.20%的遗传物质来自KOC，12.30%和11.90%的遗传物质来自BSB。RCC-L和GF-L基因组重测序的序列被定位到CC和BSB的基因组序列上，结果表明，RCC-L和GF-L与CC基因组的相似性（92.52%，90.18%）明显高于与BSB基因组的相似性（50.33%，49.18%），支持了RCC-L和GF-L的基因组主要从KOC遗传而来但含有一些来自BSB的DNA片段的观点。总体而言，我们的结果为红鲫（RCC）和GF的杂交起源提供了分子生物学证据。
