Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius

Abstract

Background: Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. Findings: A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. Conclusion: We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

“…We downloaded 26 fish genomes and 27 protein sequences of T-box family as well as seven adjacent proteins of tbx4 from NCBI (see more details in Table 3). The Chinese clearhead icefish ( Protosalanx hyalocranius ) and Northern snakehead ( Channa argus ) genomes were downloaded from GigaDB [70,71]. The genomes of spot-fin porcupinefish ( Diodon hystrix ) and river fugu ( Takifugu obscurus ) were obtained from our laboratory (unpublished data).…”

“…We then selected those with alignments to at least three adjacent genes on the same chromosome or scaffold (with tbx4 gene). Subsequently, we used Exonerate [70] and GeneWise v2.2.0 [62] to calculate the amino acid sequence of each tbx4 gene, and we corrected errors manually according to the zebrafish TBX4 protein sequence. Finally, we obtained 24 TBX4 protein sequences from 22 representative teleost fishes.…”

Genome‐wide association analyses based on whole‐genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes

“…For the sex‐associated SNPs within genes, genes boundaries were extracted from the annotation file provided by Liu et al. (2017). If the candidate SNP was not in the genic region, the gene closest to the SNP was retrieved using BEDTools v2.28.0 (Quinlan & Hall, 2010).…”

“…The generated clean reads were mapped to the draft genome of P. hyalocranius using BWA‐MEM v0.7.17 (Li, 2013) with default parameters. The draft genome assembly contains 33,609 scaffolds with a scaffold N50 size of 1.163 Mb and 19,884 predicted protein‐coding genes (Liu et al., 2017). The alignment files were processed using SAMtools v1.9 (Li et al., 2009), PCR duplications were marked using markdup function in SAMtools.…”

“…With the development of NGS technologies, whole genome sequencing and genome‐wide genetic markers are feasible at a low cost even for non‐model species. Recently, a draft genome assembly for P. hyalocranius was released with an estimated size of 525 Mb (Liu et al., 2017), which is a valuable genetic resource for revealing the mechanisms involved in sex determination and evolution of sex chromosome in the Salangid fishes.…”