[Paper Review] Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome

S. V. Shedko|arXiv (Cornell University)|Dec 5, 2019

Identification and Quantification in Food4 citations

TL;DR

This study identifies the genomic assembly ASM291031v2 (GenBank: GCA_002910315.2) as originating from Northern Dolly Varden (Salvelinus malma malma), not Arctic char (S. alpinus), despite prior assumptions. Using mitochondrial DNA (mitogenome) and nuclear markers (ITS1, RAG1, SFO-12, SFO-18, SMM-21), the analysis confirmed the female IW2-2015 specimen belonged to the BERING haplogroup and shared diagnostic alleles with Northern Dolly Varden, indicating mislabeling in the original sequencing project.

ABSTRACT

To date, twelve complete genomes representing eleven species belonging to six genera have been sequenced in salmonids. For the genus Salvelinus, it was supposed to sequence the genome of Arctic char, one of the most variable species of vertebrate animals. Sequencing was carried out (Christensen et al., 2018) using the tissues of the female IW2-2015 obtained from the company engaged in industrial aquaculture of chars - Icy Waters Ltd. The company exploits two of its own broodstocks - NL and TR, originating from the chars from the Nauyuk Lake and the Tree River (Nunavut, Canada). Since the complete mitochondrial genome of the female IW2-2015 was absent in the published assembly ASM291031v2, we determined its type and complete sequence from the sequence read archives taken from Genbank. It was found that the female's mitogenome belongs to the BERING haplogroup, which is characteristic of Northern Dolly Varden S. malma malma. Analysis of other unlinked diagnostic loci encoded by nuclear DNA (ITS1, RAG1, SFO-12, SFO-18, SMM-21) also revealed distinctive characters of Northern Dolly Varden in female IW2-2015. It was concluded that the genomic assembly ASM291031v2 was obtained not from an individual of Arctic char S. alpinus, but from an individual of a related species - Northern Dolly Varden S. malma malma. The identical to the IW2-2015 female characteristics of diagnostic loci were found in other individuals from the broodstock TR. Apparently, the broodstock TR is entirely a strain derived from Northern Dolly Varden. Since assembly ASM291031v2 was obtained from a specimen originated from the marginal population of Northern Dolly Varden (Tree R.) isolated from the main range of the species and with some traces of introgressive hybridization, this assembly can hardly be considered as a description of a typical genome of S. malma malma.

Motivation & Objective

• To resolve the taxonomic identity of the genomic assembly ASM291031v2, which was previously assumed to be from Arctic char (S. alpinus).
• To determine the true species origin of the female IW2-2015 individual used in the sequencing project.
• To assess whether the broodstock TR, from which the sample was derived, is genetically consistent with Northern Dolly Varden rather than Arctic char.
• To correct the scientific record regarding the species designation of this widely used genome assembly in salmonid genomics.

Proposed method

• Sequenced and analyzed the complete mitochondrial genome of the female IW2-2015 from SRA data in GenBank, as it was missing from the original assembly.
• Compared the mitogenome sequence to known haplogroups, identifying it as belonging to the BERING haplogroup characteristic of Northern Dolly Varden.
• Analyzed unlinked nuclear DNA markers (ITS1, RAG1, SFO-12, SFO-18, SMM-21) for diagnostic alleles specific to Salvelinus malma malma.
• Cross-referenced the genetic profiles of the IW2-2015 individual with those of other individuals from the TR broodstock to assess lineage consistency.
• Evaluated the possibility of introgressive hybridization in the isolated Tree River population to explain genetic divergence.

Experimental results

Research questions

• RQ1 Was the genomic assembly ASM291031v2 correctly assigned to Arctic char (S. alpinus), or was it mislabeled?
• RQ2 What is the true species identity of the female IW2-2015 individual used in the sequencing project?
• RQ3 Do the genetic markers (mitochondrial and nuclear) of the IW2-2015 specimen align with those of Northern Dolly Varden (S. malma malma)?
• RQ4 Is the TR broodstock, from which the sample originated, genetically consistent with Northern Dolly Varden rather than Arctic char?
• RQ5 To what extent does introgressive hybridization in the isolated Tree River population affect the genomic identity of the ASM291031v2 assembly?

Key findings

• The complete mitochondrial genome of the IW2-2015 female was determined from SRA data and found to belong to the BERING haplogroup, a hallmark of Northern Dolly Varden (S. malma malma).
• Nuclear DNA markers (ITS1, RAG1, SFO-12, SFO-18, SMM-21) in the IW2-2015 individual showed diagnostic alleles consistent with Northern Dolly Varden, not Arctic char.
• The TR broodstock, from which the sample was derived, exhibited identical diagnostic alleles to the IW2-2015 female, indicating it is entirely derived from Northern Dolly Varden.
• The genomic assembly ASM291031v2 was therefore not from Arctic char (S. alpinus), but from Northern Dolly Varden (S. malma malma).
• The specimen originated from a marginal population of Northern Dolly Varden in the Tree River, Nunavut, with evidence of low-level introgressive hybridization.
• The ASM291031v2 assembly cannot be considered a representative genome of typical S. malma malma due to its isolated, possibly hybridized lineage.