Jonathan Kreplak, Mohammed-Amin Madoui, […], Judith Burstin

Nature Genetics volume 51, pages 1411–1422 (2019)

ABSTRACT

Pea (Pisum sativum L., 2n = 14) is the second most important grain legume in the world after common bean and is an important green vegetable with 14.3 t of dry pea and 19.9 t of green pea produced in 2016 (http://www.fao.org/faostat/). Pea belongs to the Leguminosae (or Fabaceae), which includes cool season grain legumes from the Galegoid clade, such as pea, lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), faba bean (Vicia faba L.) and tropical grain legumes from the Milletoid clade, such as common bean (Phaseolus vulgaris L.), cowpea (Vigna unguiculata (L.) Walp.) and mungbean (Vigna radiata (L.) R. Wilczek).

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

See https://www.nature.com/articles/s41588-019-0480-1

Figure 1: a, Circos view of the pea genome. Pseudomolecule color-code is shaded at estimated centromere positions. Lanes depict circular representation of pseudomolecules (a) and the density of retrotransposons, transposons, genes, ncRNA, tRNA and miRNA coding sequences (b–g). Lines in the inner circle represent links between synteny-selected paralogs. b, Estimated positions of centromeres in the assembly and their comparison to pea cytogenetic map is schematically represented, with pseudomolecules as white bars and cytogenetic maps of pea chromosomes as gray bars. Non-recombining regions representing the centromeres are marked in green. Positions of centromeric single-copy FISH markers are indicated above the pseudomolecules in black and positions of arrays of centromeric satellites present in the assembly are shown below them in blue. Positions of primary constrictions on the cytogenetic maps are labeled in red. PisTR-B satellite loci used to discriminate individual chromosomes are shown in purple boxes on the gray bars. c, FISH localization of the satellite repeats TR11/19 (red) and TR10 (green) on metaphase chromosomes (gray). d, Discrimination of chromosomes within the pea karyotype using FISH with PisTR-B probe (purple). e, Example of FISH detection of the single-copy marker (1722, green) in the centromere of chromosome 6. f, Chromosome 6 with labeled centromeric repeat TR11/19. g, The density of different TE lineages inferred from the detection of their protein-coding domains along pseudomolecules.