Chromosome-Scale Assembly and Characterization of the Albino Northern Snakehead, Channa argus var. (Teleostei: Channidae) Genome

Abstract

Northern snakehead, Channa argus (C. argus), is an important economic and ecological fish species. The wild population of the species was sharply declined in the last decade. A high-quality reference genome could lay a solid foundation for the genetic and conservation studies for C. argus. In this work, we report a chromosomal genome assembly with PacBio and Hi-C technology using the albino northern snakehead, a color variety of C. argus. A 644.1-Mb genome with 24 chromosomes was obtained with a contig and scaffold N50 of 11.78 and 27.8 Mb, respectively. We inferred that C. argus diverged from A. testudineus around 85.6 million years ago. 514 expanded gene families and 214 positively selected genes were identified in the C. argus genome. The chromosome-level genome provides a valuable high-quality genomic resource for population, as well as genetic and evolutionary studies for C. argus and other species in Channidae.

Klumpy: A Tool to Evaluate the Integrity of Long-Read Genome Assemblies and Illusive Sequence Motifs

“…In our second example, we examined the reported absence of the adenylate cyclase 5 ( adcy5 ) gene in a new, long-read-based assembly of the albino northern snakehead ( Channa argus ) genome (Zhou et al 2022). The adcy5 gene has been previously noted as having a functional role in guppy ( Poecilia reticulata ) pigmentation (Kottler et al 2015), and its putative absence in the albino northern snakehead genome may reflect a similar effect on the organism’s phenotype.…”

“…2). When we searched for a possible explanation to determine why the gene was reported absent by Zhou et al (2022), we located an alternative codon, annotated in the albino reference but not in the non-albino reference, that contained a putative premature stop codon 528 bases upstream from the exon 1 klump (Fig. 2).…”

“…Given that the two genome assemblies were annotated using two different annotation pipelines and data, it is plausible that some genes may have been annotated in one assembly and left unannotated in the other. Another cause for the reported absence of the adcy5 gene could be the specific gene identification methodology the authors applied, in which genome specific (i.e., non-albino vs albino phenotype) genes were determined by identifying genes with less than 80% overlap between coding sequences obtained from the two assemblies (Zhou et al 2022). By using a shortened coding sequence of the adcy5 , the adcy5 gene would have been reported absent following the above approach.…”

“…The raw reads tiled across the entire adcy5 gene and the nearest gap was located over 5.7 Mb away from the adcy5 klumps. Furthermore, we were unable to replicate the syntenic region presented by Zhou et al (2022) using Klumpy (Figs S6 and S7; Text S2). Regardless of these findings, a complete adcy5 gene was located in the albino northern snakehead genome, supporting the findings by Sun et al (2023).…”

“…The alignments were then sorted and indexed using Samtools (Li et al 2009). Additionally, we used MUSCLE (Edgar 2004) to perform a local alignment between the two northern snakehead reference genomes upstream of the exon 1 klump to identify mechanisms that may have attributed to the findings of Zhou et al (2022). Lastly, to reproduce the findings of Zhou et al (2022), we repeated the ‘find_klumps’ analysis with the Illumina-based northern snakehead assembly.…”