title: Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula.
abstract: Schrenkiella parvula (formerly Thellungiella parvula), a close relative of Arabidopsis (Arabidopsis thaliana) and Brassica crop species, thrives on the shores of Lake Tuz, Turkey, where soils accumulate high concentrations of multiple-ion salts. Despite the stark differences in adaptations to extreme salt stresses, the genomes of S. parvula and Arabidopsis show extensive synteny. S. parvula completes its life cycle in the presence of Na⁺, K⁺, Mg²⁺, Li⁺, and borate at soil concentrations lethal to Arabidopsis. Genome structural variations, including tandem duplications and translocations of genes, interrupt the colinearity observed throughout the S. parvula and Arabidopsis genomes. Structural variations distinguish homologous gene pairs characterized by divergent promoter sequences and basal-level expression strengths. Comparative RNA sequencing reveals the enrichment of ion-transport functions among genes with higher expression in S. parvula, while pathogen defense-related genes show higher expression in Arabidopsis. Key stress-related ion transporter genes in S. parvula showed increased copy number, higher transcript dosage, and evidence for subfunctionalization. This extremophyte offers a framework to identify the requisite adjustments of genomic architecture and expression control for a set of genes found in most plants in a way to support distinct niche adaptation and lifestyles.
authors.affiliation: Department of Biology, Louisiana State University, Baton Rouge, Louisiana 70803.
authors.forename: Dong-Ha
authors.initials: DH
authors.lastname: Oh
authors.forename: Hyewon
authors.initials: H
authors.lastname: Hong
authors.forename: Sang Yeol
authors.initials: SY
authors.lastname: Lee
authors.forename: Dae-Jin
authors.initials: DJ
authors.lastname: Yun
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Bohnert
authors.forename: Maheshi
authors.initials: M
authors.lastname: Dassanayake
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics*; D017360:Arabidopsis / Q000502:physiology; D019607:Brassicaceae / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D020440:Gene Duplication / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D017136:Ion Transport / Q000187:drug effects / Q000235:genetics; D007477:Ions / Q000494:pharmacology*; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012492:Salts / Q000494:pharmacology; D012689:Sequence Homology, Nucleic Acid; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D007477:Ions; D026901:Membrane Transport Proteins; D010940:Plant Proteins; D012492:Salts