A Homology Guide for Pacific Salmon Genus Oncorhynchus resolves patterns of Duplicate Retention, Rediploidization and Local Adaptation Following the Salmonid Specific Whole Genome Duplication Event

Abstract

Salmonid fishes have emerged as a tractable model to study whole genome duplications (WGD) as this group has undergone four rounds of WGD, with a significant proportion of the genome yet to rediploidize. The fact that much of modern salmonid genomes retain duplicates from the most recent WGD while other regions have rediploidized creates complications for genetic studies by obscuring homology relationships and the necessity of filtering duplicate regions from many analyses. The difficulty this creates is particularly prominent in Pacific salmonids genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural role these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of duplicate retention and rediploidization. Overall, we find that retained duplicates comprise over half of modern gene repertoires and that retained duplicate genes are enriched for genes involved in nuclear stability, while rediploidized genes which represent a smaller proportion of genes are heavily enriched in dosage sensitive processes such as mitochondria. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss we demonstrate that retained duplicates are more likely to be associated with adaptive divergence than rediploidized genes, highlighting the potential of WGDs to promote adaptation. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life history traits or gene editing targets.

Local Thermal Adaptation occurs via Modulation of Mitochondrial Activity in Chinook Salmon

“…Read counts were enumerated with Salmon V1.8.0 (Patro et al, 2017), the salmon index was generated from the O. tshawytscha transcriptome (Otsh_v2.0) and decoys were constructed by concatenating the O. tshawytscha genome (Otsh_v2.0) (Christensen et al, 2018) to the end of the transcriptome and using the genomic contigs names as decoys. We used a K-mer size of 31 which our previous work has shown to be sufficient for differentiating between transcripts with low sequence divergence such as ohnologs or paralogs which are common in Salmonid genomes (Dimos & Phelps, 2022). Read mapping rates averaged 73.2% resulting in an average coverage of 965 mapped reads/gene.…”

Polyploid plants take cytonuclear perturbations in stride

“…Multiple studies have detected biased retention patterns for these gene classes in polyploid plants (Coate et al, 2011;De Smet et al, 2013;Li et al, 2016;Tasdighian et al, 2017;Emery et al, 2018;Ferreira de Carvalho et al, 2019;Sharbrough et al, 2022) and other eukaryotes (Wapinski et al, 2007;Conant, 2014;Session et al, 2016;Li et al, 2018;Dimos and Phelps, 2023). These biases, however, have been in different directions depending on the specific choice of loci, taxa, and temporal scale of analysis.…”