Zaragoza, December, 21st, 2017.
The pangenome of a species is the sum of all genetic material of all individuals from that species. While most described pangenomes are from microorganisms, two recent papers reveal for the first time the dimensions of pangenomes of non-cultivated plants, and tell part of its evolutionary history. These works study a modest wild grass, Brachypodium distachyon, which has a genome an order of magnitude smaller than its relatives barley and wheat. In particular, the team of researchers collected plants from 54 locations around the Mediterranean sea and sequenced their nuclear and chloroplastic genome, the latter from the green organelles where photosynthesis occurs. The findings of both works can be summarized as follows:
First, though each sequenced plant encodes 31,000 genes, the pangenome contains over 60,000, of which about a third are common to all individuals. These numbers demonstrate a great variability in gene number, as well as in DNA content, among individuals of the same species. While core genes have essential biological functions, accessory genes, found only in some individuals, seem to have conditionally beneficial roles in processes such as development and defense. Moreover, accessory genes are generally located near transposons, which have often been considered “genomic junk”.
Second, the sampled natural populations of Brachypodium distachyon differ in their flowering patterns, requiring more or less vernal days in order to flower, as seen also in wheat and barley varieties. This behavior correlates both with differences at the pangenome level, gene subsets shared by populations with similar flowering phenotypes, and mutations in genes known to control flowering in other grasses, such as VRN1 or FTL.
Third, the comparison of nuclear and plastid genomes confirms that flowering time has driven evolution within this species, and revealed that different populations have interchanged chloroplasts. This indicates that the evolutionary histories told by the nuclear and the chloroplast genomes are complementary and that neither is complete without the other.
Several researchers from Universidad de Zaragoza, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas and Fundación ARAID have participated: Rubén Sancho, Carlos Pérez Cantalapiedra, Diana López, Pilar Catalán and Bruno Contreras Moreira.
Gordon SP, Contreras-Moreira B, Woods DP, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin AC, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Budak H, Juenger TE, Amasino R, Caicedo, AL, Goodstein D, Davidson P, Mur LAJ, Figueroa M, Freeling M, Catalan P, Vogel JP. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications 8: 2184 (2017) ► (Open Access)
Sancho R, Cantalapiedra CP, López-Álvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. Comparative plastome genomics and phylogenomics of Brachypodium: Flowering time signatures, introgression and recombination in recently diverged ecotypes [Epub ahead of print] New Phytologist (Available online Dec 2017) (DOI: 10.1111/nph.14926) ►
Phylogenomic tree of 54 ecotypes of Brachypodium distachyon from around the Mediterranean sea, evolutionary placed in 3 groups [extremely delayed flowering (EDF+, blue), wastern Mediterranean (T+, yellow), western Mediterranean (S+, green)] related to their flowering pattern and geographic distribution. Ecotype Bd21, whose genome serves as a reference for this species, is marked with a star in the map. The Venn diagram shows the number of genes shared by sequenced genomes of non-admixed ecotypes of these groups (genetic structure represented as vertical coloured vertical bars) and also genes exclusive to each group.