Problems with Paralogs: The Promise and Challenges of Gene Duplicates in Evo-Devo Research

Abstract

Gene duplicates, or paralogs, serve as a major source of new genetic material and comprise seeds for evolutionary innovation. While originally thought to be quickly lost or nonfunctionalized following duplication, now a vast number of paralogs are known to be retained in a functional state. Daughter paralogs can provide robustness through redundancy, specialize via sub-functionalization, or neo-functionalize to play new roles. Indeed, the duplication and divergence of developmental genes have played a monumental role in the evolution of animal forms (e.g., Hox genes). Still, despite their prevalence and evolutionary importance, the precise detection of gene duplicates in newly sequenced genomes remains technically challenging and often overlooked. This presents an especially pertinent problem for evolutionary developmental biology, where hypothesis testing requires accurate detection of changes in gene expression and function, often in nontraditional model species. Frequently, these analyses rely on molecular reagents designed within coding sequences that may be highly similar in recently duplicated paralogs, leading to cross-reactivity and spurious results. Thus, care is needed to avoid erroneously assigning diverged functions of paralogs to a single gene, and potentially misinterpreting evolutionary history. This perspective aims to overview the prevalence and importance of paralogs and to shed light on the difficulty of their detection and analysis while offering potential solutions.

Fig. 1

Similarities and differences among pea aphid fs paralogs. (A) Diagram of the gene structures of fs paralogs. Transcriptional start sites are marked with arrows, exonic sequences are represented by vertical bars, and introns are depicted as horizontal lines. Scale bar: 10 kb. Changes that have occurred in intronic sequences are evident in differential spacing of exons between paralogs. (B) Alignment of fs-2 and fs-3 mRNA sequences (tan arrows) to that of fs-1. Red shading of fs-2 and fs-3 indicates sequence conservation with fs-1. The coding sequence of fs-1 is shown as a maroon arrow. While mismatches are present within the coding region, sequence is dramatically less conserved in the noncoding 5′- and 3′-untranslated regions (UTRs). Scale bar: 200 nt. (C) Amino acid alignment of fs paralogs. Conserved residues are highlighted in yellow. A conservation track is shown above the aligned residues in which darker shades of gray or black indicate increasing or perfect sequence identity, respectively. Aside from the N- and C-termini, all three protein sequences are highly similar. Alignments were performed and visualized using SnapGene^® software (from Dotmatics; available at snapgene.com).