NEW YORK (GenomeWeb) – In a Nature Genetics paper appearing online today, an international team described findings from an effort to sequence and analyze the genomes of two diploid plants that are believed to be the ancestors of the cultivated allotetraploid peanut plant, Arachis hypogaea.
"The availability of these genomes will lead to further advances in knowledge of genetic changes since the very recent polyploidization event that gave rise to cultivated peanut and to the production of better tools for molecular breeding and crop improvement," the study's authors wrote.
The effort focused on the genomes of A. duranensis and A. ipaensis, which were expected to somewhat resemble the cultivated peanut's A and B sub-genomes. But when they sequenced the genomes of the two diploid plants, the researchers found that one of them — the A. ipaensis plant collected from small, isolated population in Bolivia in the 1970s — was nearly identical to the A. hypogaea plant's B sub-genome, providing clues to the legume's probable origins in South America and its domestication history.
"It's almost as if we had traveled back in time and sampled the same plant that gave rise to cultivated peanuts from the gardens of these ancient people," co-first author David Bertioli, a plant geneticist affiliated with the University of Brazil and University of Georgia, said in a statement.
The first archeological evidence of allotetraploid A. hypogaea peanut plant cultivation goes back some 3,500 to 4,500 years, the team noted, though cultivation of other Arachis species seems to stretch back much further than that in South America.
In an effort to better understand peanut biology and origins, members of the International Peanut Genome Initiative used a combination of Illumina HiSeq 2000 paired-end short reads and Moleculo long reads to assess DNA from an A. duranensis V14169 accession collected in Argentina in 1997 and an A. ipaensis accession called K30076 from Bolivia.
The team's analysis uncovered 6,241 predicted protein-coding genes in the 1.2 billion base A. duranensis genome, covered to an average depth of 154-fold, and an estimated 7,825 A. ipaensis protein-coding sequences in that plant's 1.5 billion base genome, covered to 163-fold, on average.
Transposable elements made up nearly 62 percent of the A. duranensis genome, whilemore than 68 percent of the A. ipaensis genome was made up of transposable elements. The researchers noted that most of the transposon families overlapped between the A. duranensis and A. ipaensis plants.
Along with an analysis of potential disease resistance genes, the team used MethylC bisulfite sequencing to assess DNA methylation profiles in the diploid legume plants.
From predicted mutation rates in A. duranensis and A. ipaensis relative to other legume plants, together with chromosomal synteny patterns and low-coverage Moleculo-based genome sequence data for A. hypogaea, the researchers retraced relationships between the diploid plants and sequences in the cultivated peanut A and B genomes — for instance, A. ipaensis' near-identical similarity to the cultivated peanut's B sub-genome.
Because the reproductive features of peanut plants limit their dispersal to less than a mile per thousand years, the team estimated that ancestral plant seeds transported by human some 10,000 years ago led to the hybridization of A. ipaensis and A. duranensis in a region near the Bolivia-Argentina border.
"It's the only place where A and B genome species have ever been found growing close together," Bertioli said in a statement. "The region is right next to the region where … the most primitive types of cultivated peanut are grown, and the date is right in the time frame that plant domestication was happening in South America."