Abstract Detail

Molecular Ecology

Hawkins, Angela [1], Pepper, Alan [1].

RNA-Seq analysis reveals novel insights into serpentine tolerance in Caulanthus amplexicaulis var. barbarae (Brassicaceae).

Serpentine endemic plants are excellent models for the study of molecular evolution as they provide extreme examples of adaptation to environment. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g. N, P, K, Ca), as well as toxic levels of heavy metals (e.g. Ni, Cr, Co), and very poor moisture availability. These outcrops provide habitat to the endemic plant species, Caulanthus amplexicaulis var. barbarae (J. Howell) Munz ("Cab"). Its sister species, C. amplexicaulis var. amplexicaulis S. Watson (Caa), is found predominately on granite soils and is intolerant to serpentine soils. Comprehensive reference transcriptomes and genomes of both Caa and Cab are available for use in protein coding gene comparisons. Both common garden on ¼ strength MS media and reciprocal transplant experiments on natural granite and serpentine soils were performed using Caa, Cab, and a F1 hybrid. RNA-seq analyses were implemented to calculate global expression patterns and identify differentially regulated gens that may play a role in serpentine adaptation. Gene expression levels were calculated as transcripts per million (TPM) by the program Salmon using the CAB1 genome assembly as reference and paired end fastq files of RNA-seq data from all replicates in all growth conditions. EdgeR was then used to calculate log fold change for all genes. Weighted correlation network analysis (WGCNA) was performed to cluster all genes based on their expression profile. In all, the data was separated into 18 modules (clusters) based on similar expression levels. These modules were further processed using fisher's exact test to find any overrepresented GO terms. Initial efforts were set out to answer the following three questions: which genes are constitutively expressed in Cab, which genes are induced in Cab on serpentine outcrops, and which genes are induced in Caa on serpentine outcrops? RNA-seq data implicates a suite of photosynthesis genes being constitutively expressed in Cab, this is an unexpected and novel finding. Genes induced in Cab on serpentine include those with roles in nutrient acquisition and movement and heavy metal binding, and genes induced in Caa on serpentine indicate response to nutrient starvation and galactose binding/transport. Ultimately results from these analyses, in conjunction with coding sequence data and QTL mapping, will be used to find high quality candidate genes that confer tolerance to serpentine soils.

1 - Texas A&M University, Department Of Biology, 3258 TAMU, College Station, TX, 77843, United States

Keywords:
Serpentine
Caulanthus
RNA-Seq
Brassicaceae.

Presentation Type: Oral Paper
Session: 22, Molecular Ecology
Location: 107/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 11:00 AM
Number: 22011
Abstract ID:847
Candidate for Awards:None