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Arabidopsis Studies Tap 1,001 Genomes Data to Explore Genomic, Epigenomic, Speciation History

NEW YORK (GenomeWeb) – A handful of recent studies are highlighting the genomic patterns, epigenomic diversity, and speciation history of the model plant Arabidopsis thaliana.

An international team led by investigators at the Salk Institute for Biological Studies published two papers online last week in Cell. For one of the studies, the group described more than 10.7 millions SNPs and 1.4 million small insertions and deletion polymorphisms it identified by sequencing the genomes of 1,135 naturally-occurring Arabidopsis accessions from Eurasia, North Africa, and North America from the 1,001 Arabidopsis thaliana Genomes collection.

The variants provided a peek at the plant's population structure, past geographic dispersal patterns, and local adaptations. They are expected to facilitate future genome-wide association studies, co-corresponding author Detlef Weigel, a researcher with the Max Planck Institute for Developmental Biology, and his co-authors explained.

"Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes," they wrote.

In a related Cell study, Weigel and other members of the 1001 Genomes Consortium team presented findings from an analysis of DNA methylomes and transcriptomes for Arabidopsis representatives from the 1001 Genomes Project.

There, the researchers used MethylC-seq bisulfite sequencing to interrogate cytosine methylation at the single-base level in 1,107 Arabidopsis accessions, uncovering more than 22,000 differentially-methylated regions of the genome, depending on the accession considered. They also profiled more than 1,200 Arabidopsis transcriptomes with RNA sequencing, providing insights on expression of 18,000 genes per accession, on average.

By bringing together the genomic, epigenomic, and transcriptomic clues from this large A. thaliana collection, the researchers were able to begin interpreting interactions between specific genes, genetic variants, epigenetic marks, and gene expression patterns.

"There are genes that control the epigenome in these various plants," Joseph Ecker, a plant biology researcher at the Salk Institute and senior author on the epigenetic paper, said in a statement, "and variants of those genes potentially alter the epigenome in a way that helps the plant survive better in a particular environment."

"Breeders could potentially use epigenetic information just like they use genetic information to select for traits; the power of such an approach can now be tested," Ecker explained. "Beyond individual genes being useful, the idea that there are epigenetic variants that could be selected for is something that they should pay attention to."

Finally, some of the same investigators explored the speciation history of the Arabidopsis genus for a Nature Genetics study out online today. By re-sequencing 94 plants, including multiple representatives apiece from 27 Arabidopsis taxa, that team identified seven SNP-based clusters, coinciding with known species in the genus.

Even so, a closer look at the polymorphism patterns and a gene-level comparison of the plants — helped along by genome maps and SNP calls generated for the 1,001 Genomes Project — suggested Arabidopsis speciation followed a non-bifurcating model rather than a typically branching phylogenetic tree.

"[W]e would argue that speciation in this genus is a protracted process involving selection and long periods of partial isolation between incipient species," the study's senior author Magnus Nordborg, director of the Gregor Mendel Institute at the Austrian Academy of Sciences, and his colleagues explained.