Genome Structures and Transcriptomes Signify Evolutionary Trajectories for Multi-Ion Tolerance and Niche Adaptation in Schrenkiella parvula (formerly Thellungiella parvula)

Schrenkiella parvula (Thellungiella parvula), a close relative of Arabidopsis and Brassica crops, thrives in the shores of Lake Tuz, Turkey, where soils accumulate high concentrations of multi-ion salts. Despite the stark differences in adaptations to extreme salt stresses, genomes of S. parvula and Arabidopsis thaliana show overall high synteny.

            S. parvula completes its life cycle in the presence of Na⁺, K⁺, Mg²⁺, Li⁺ and borate at concentrations lethal to A. thaliana. Explicit genome structural variations, including tandem duplications and translocations of genes, interrupt the co-linearity observed throughout the genomes of S. parvula and A. thaliana, and increased promoter sequence divergence. Inter-species comparative RNA-seq revealed clusters of homologous gene pairs showing distinct responses to salt stress in the two species. In addition, about 17% of total homologous gene pairs showed significantly different basal-level expressions between S. parvula and A. thaliana. Ion-transport functions were enriched among genes with higher basal-level expression in S. parvula, while defense-related genes showed higher expression in A. thaliana. Duplication of key stress-related ion transporter genes in S. parvula resulted in sub-functionalization and increased basal-level transcript dosages.

            We found in Schrenkiella parvula the most lucid account of indispensable adjustments in a set of genes that - although present in most or all plants - enable its extremophyte lifestyle. Modifications of genome structures and, in turn, transcriptome expression profiles, lead the two closely-related species, S. parvula and A. thaliana to distinct phenotypes and niche adaptations.