High-quality genome assembly and annotation of the big-eye mandarin fish (Siniperca knerii)

Abstract

The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka - 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.