Phylogenetic history of Chinese goldfish based on gene enrichment data

Abstract:

Goldfish， is an ornamental fish originated in China， which was domesticated from wild crucian carp. There are great differences between different types of goldfish， such as presence or absence of dorsal fin， telescope or bubble eyes， oranda and other characters. Long-term hybridization and artificial selection have produced a large number of goldfish strains， but it also leads to the confusion and complexity in determining pedigree relationship of goldfish， which makes it more difficult to distinguish goldfish strains. People tried many ways to clarify the pedigree history and hybridization relationship between various goldfish strains， but so far no progress has been made. That is why the selection history of most goldfish strains has not been clarified and the hybridization relationships of many goldfish strain have not been confirmed. In this study， tissue samples of 59 individuals from 11 Chinese goldfish strains were collected. Cross-species target gene enrichment and high-throughput sequencing were used to obtain the target gene sequencing data of each goldfish individual. Using 4 434 single-copy gene loci of zebrafish as reference sequences， the corresponding goldfish genes were grouped according to its heterotetraploid subgenome， and the enriched sequences were compared and categorized according to two subgenomes respectively. A total of 35 298 single nucleotide polymorphism （SNPs） loci were called， which were used to study the pedigree history and hybridization relationship of the goldfish strains. Principal component analyses， genetic structure analyses and phylogenetic network map of the two subgenomes were reconstructed to reveal genetic relationship of these Chinese goldfish strains and explain their selection and hybridization history： （1） The telescope and Ryukin were directly evolved from the wakin， while pearlscale and lionhead were not directly evolved from the wakin. （2） Ranchu evolved earlier than egg bubble eye， while the bubble eye had secondly lost its dorsal fin. （3） The telescope-oranda is closely related to the lionhead， which first generated the character of oranda， and later obtained the telescope eyes. （4） Pearlscale， pearlscale-oranda and telescope-pearlscale-oranda are genetically similar. Pearlscale-oranda directly evolved from pearlscale， telescope-pearlscale-oranda is the latest bred form， probably a hybrid of telescope and pearlscale-oranda. The results of this study may help to understand the evolution history of Chinese goldfish and provide some reference for the classification and breeding of goldfish varieties.