Abstract
The
Oryza officinalis
complex is the largest species group in
Oryza
, with more than nine species from four continents, and is a
tertiary gene pool that can be exploited in breeding programs for the improvement of
cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using
a new reference C genome for the diploid species
O. officinalis
, and
draft genomes for two other C genome diploid species
Oryza eichingeri
and
Oryza rhizomatis
, we examine the influence of transposable elements on
genome structure and provide a detailed phylogeny and evolutionary history of the
Oryza
C genomes. The
O. officinalis
genome is 1.6
times larger than the A genome of cultivated
Oryza sativa
, mostly due to
proliferation of
Gypsy
type long-terminal repeat transposable elements,
but overall syntenic relationships are maintained with other
Oryza
genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species,
Oryza eichingeri
and
Oryza rhizomatis
, and short-read
resequencing of a series of other C genome species and accessions reveal that after the
divergence of the C genome progenitor, there was still a substantial degree of variation
within the C genome species through proliferation and loss of both DNA and long-terminal
repeat transposable elements. We provide a detailed phylogeny and evolutionary history of
the
Oryza
C genomes and a genomic resource for the exploitation of the
Oryza
tertiary gene pool.