Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Abstract

Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.

Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species

“…This is in agreement with high expression specificity of LSGs during the development of Dictyostelid slime molds. 12 This trend is mostly driven by the broad expression of shared genes: LSGs were always significantly more narrowly expressed compared to shared genes (Mann-Whitney U-test FDR-corrected P -value < .05) but only sometimes compared to tardigrade-specific genes ( Figure 2 ). LSGs were significantly more narrowly expressed than TSGs in both species in 4 comparisons: first day egg, first day juveniles, and in both active and tun adults.…”

“…These results support recent findings from slime molds, in which shared singletons were underrepresented among biased genes whereas LSGs (as well as shared paralogs) were enriched among biased genes. 12 The differences in expression bias of LSG paralogs between He and Rv (Figure 3; Supplemental Figure S4B) suggest that the evolution of expression specificity of recently duplicated genes in the 2 species targets different developmental pathways. Biased genes largely displayed different enriched gene ontology (GO) terms between tardigrade species, except for juvenilebiased genes that were enriched with chitin binding genes (Figure 4).…”

“…10,11 The analysis of expression profiles throughout development in C. elegans found an enrichment of younger genes in late embryogenesis, 11 while in slime molds LSGs were found predominantly biased during the middle stages of development. 12 But compared to tissue-specific expression, very little is known regarding expression bias of new genes across developmental stages and physiological states, or how this varies among species.…”

Whole‐genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines

“…muticum and wheat genes. However, some of this relationship could be driven by the confounding effect of more conserved genes having more core functions and therefore being more constitutively expressed (Luna and Chain, 2021 ). It will be important to explore this further to begin to determine whether traits identified in wild relatives may present differently when introgressed into wheat.…”

Evolutionary New Genes in a Growing Paradigm

“…In an organism that contributed to the understanding of the origination of multicellularity, Luna and Chain [ 19 ] reported an exciting discovery from analyses of five dictyostelid species genomes, i.e., 24% of genes in the genomes are lineage- or species-specific. Further analyses indicate that the biased new gene duplicates, expressed in a particular developmental stage, show greater divergence in expression among orthologues and paralogues.…”