Perenniality, abiotic stress tolerance, and biomass allocation in Brachypodium, a model grass genus for bioenergy

The grass Brachypodium distachyon is a well-developed model genomic system for
studying the genetic, developmental, and physiological basis of biofuel feedstock
production. Recent work on a second species, B. sylvaticum, has extended the tremendous
value of Brachypodium for improving biofuel crops due to its perennial life history.
Successfully translating research from these two species to biofuel crops requires a
fundamental understanding of how plants make decisions about the allocation of
meristems and biomass to vegetative and reproductive growth. We propose a series of
comparative genomic analyses with the broad aim of identifying transcripts and putative
regulatory control elements (conserved non-coding sequences; CNS) that are associated
with the evolutionary transition between annual and perennial life history strategies. We
will accomplish this via de novo sequencing of additional perennial Brachypodium
species and a new outgroup species to facilitate phylogenomic analysis, deep
resequencing of natural accessions of B. sylvaticum, and an RNASeq experiment
assessing transcriptional control of meristem transitions in annual and perennial species
of Brachypodium. In addition to allowing us to test hypotheses related to the
environmental and genetic control of biomass partitioning, the new sequence data
generated will provide an unprecedented set of community resources for comparative
genomic analysis in the grasses.

Scope of Work:
Two sets of genomic sequencing are proposed. First, we propose comparative-grade de
novo genome sequencing of four grass species; three of these are diploid species and the
fourth is a tetraploid that is closely related to the JGI flagship B. distachyon. This part of
the project will require ~470GB of sequencing. Second, we propose deep resequencing of
25 natural accessions of diploid B. sylvaticum. This part of the project will require
~400GB of sequencing. We also propose an RNASeq study of five species of
Brachypodium, all of which presently have high-quality draft or complete reference
genomes available, or are species for which we will generate genomes in the current
project. This part of the project will require ~150GB of sequencing.
We propose that JGI prepare sequencing libraries, perform short-read sequencing
(or long-read PacBio for the de novo genomes, if possible), and assemble and annotate
the genome sequences. We will provide reference transcriptomes to aid in annotation. For
the RNASeq experiment, we propose that JGI map the reads to reference genomes and
provide tables of feature counts. JGI has been instrumental in past Brachypodium genome
sequence and analysis through its development of reference genomes for B. distachyon,
B. stacei, B. hybridum, and B. sylvaticum and deep re-sequencing of B. distachyon natural
accessions. As such, JGI possesses un-matched expertise in working with the genomes of
this important reference genus. Members of the current CSP team have collaborated with
JGI on aspects of each of these earlier projects.

Contreras Moreira, Bruno
Principal researcher: 
Bruno Contreras-Moreira (coIP), David Des Marais (IP)
Managing entity: 
Number of researchers: 
Start date: 
End date: 
Entidad financiadora
Financing entity: 
DOE Joint Genome Institute, USA
Community Science Program 2016