RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish

Area of Science:

• Genomics
• Evolutionary Biology
• Ecology

Background:

• Messenger RNA (mRNA) sequencing is increasingly used for gene expression studies in non-model species.
• Its potential extends to analyzing alternative splicing, population structure, and selection signatures.
• Combining these analyses can reveal dynamics between gene expression, selection, and population structure.

Purpose of the Study:

• To compare population structure and genetic variation derived from mRNA sequencing with microsatellite data.
• To investigate phenotypic plasticity and evolutionary signatures using whole transcriptome data.
• To explore the interplay between gene expression, plasticity, and selection in adaptation.

Main Methods:

• Whole transcriptome mRNA sequencing of two minnow populations (Sacramento splittail) under salinity challenge.
• Comparison of single nucleotide polymorphisms (SNPs) from mRNA data with microsatellite data for population structure.
• Analysis of differential gene expression, exon usage, and gene expression variation for plasticity.
• Outlier SNP analysis to detect signatures of selection.

Main Results:

• mRNA sequencing identified population structure consistent with microsatellite data, albeit with lower genetic variation.
• Purifying selection likely explains the reduced variation observed in mRNA data.
• Phenotypic plasticity and selection signatures were largely mutually exclusive within individual genes, with few exceptions.

Conclusions:

• mRNA sequencing data offers multiple applications, including population structure description and evolutionary studies.
• It provides insights into the interplay between plasticity and evolution in adaptation.
• mRNA sequencing complements traditional population genetics methods and enhances the study of phenotypic plasticity.