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International Group Sequences Genome of Arabidopsis Relative Adapted to Extreme Conditions

By Andrea Anderson

NEW YORK (GenomeWeb News) – Researchers reported in Nature Genetics online yesterday that they have sequenced the genome of a plant called Thellugiella parvula, which is related to the model organism Arabidopsis thaliana but is adapted to much more extreme conditions.

"It is generally more tolerant to every kind of stress — salt tolerance, heat stress, and also drought," co-first author Dong-Ha Oh, a post-doctoral researcher in Han Bohnert's plant biology lab at the University of Illinois at Urbana-Champaign, told GenomeWeb Daily News.

"Arabidopsis thaliana has been well studied," he added, "but it doesn't have any kind of stress tolerance."

Oh and his colleagues from the US, Korea, and Saudi Arabia used high-throughput sequencing to sequence the draft genome of T. parvula. By comparing it with genome and transcriptome sequences from A. thaliana, they found clues about the genetic strategies that T. parvula uses to survive extreme conditions. Among them: a preponderance of duplications involving stress response and other genes.

Using DNA from a T. parvula plant collected from a salt lake in central Turkey, the researchers generated genome sequence reads covering the plant's 140 million base genome to a depth of about 50 times with a combination of Roche 454 GS FLX Titanium and Illumina GAII sequencing.

T. parvula belongs to a plant group from which A. thaliana is thought to have diverged around 43 million years ago. But despite their relatively close relationship, the two plant species have far different abilities to withstand salinity and other stressful conditions.

"The availability of the T. parvula genome provides a unique view of chromosome structure, organization, and gene complement," the researchers wrote. "Of particular importance is the comparison of this genome with that of the related A. thaliana, which is unquestionably a stress-sensitive species."

Relying on an iterative hybrid approach — which involved cobbling together sequence backbones from longer Roche 454 reads, filling in gaps with deep coverage Illumina reads, and using reads from each platform to correct the other — the team assembled nearly 1,500 meta-contigs of T. parvula sequence, each between 1,000 and more than 13 million bases long.

"Many of the biggest contigs are chromosome arm size," Oh said. "So we could assemble the chromosomes just using next-generation sequencing tools."

When they analyzed this draft genome, the team found an estimated 28,901 protein-coding sequences, compared with the 27,059 reported for A. thaliana, which has a genome that's around 15 percent smaller.

More than 19,000 of the predicted open reading frames in the new genome coincided with transcriptome sequences from various T. parvula tissues. And overall, the team reported that 53 percent of the T. parvula genes that they searched in NCBI's BLASTn database were most similar to A. thaliana sequences.

At first glance, the gene composition of the two genomes was very similar, Oh said, though he noted that he and his colleagues found subtle differences as well.

Notably, although the T. parvula and A. thaliana genomes contain a similar number of genes that had undergone tandem duplications, only half of the duplicated genes overlap between the two plant species. Instead, the T. parvula genome seems to contain far more duplications involving genes predicted to contribute to stress adaptation or with unknown functions.

Additional comparisons to the A. thaliana transcriptome data hinted that the T. parvula genome also houses an over-representation of some developmental, abiotic and biotic stimulus response, and transporter genes. On the other hand, researchers reported, it seems to contain fewer signal transduction genes than Arabidopsis.

The researchers are continuing to study genome, gene, and protein patterns that may lend T. parvula stress-tolerance advantages over A. thaliana, Oh said, including studies looking specifically at genes that increase A. thaliana stress sensitivity when mutated. Preliminary results suggest that some of these stress tolerance genes show distinct copy number, promoter, expression, and protein function patterns in T. parvula, he said.

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