The pangenome of Brachypodium distachyon: estimating the true genomic diversity of a species
Researcher:
Contreras Moreira (on leave since 30/09/2018) , Bruno
The genetic diversity of a species is the sum of the diversity found in all individuals of that
species. Many studies have attempted to estimate the diversity of a species by resequencing
diverse accessions and aligning the reads to a reference genome. While this approach readily
identifies SNPs and small indels, it underestimates total genomic diversity because highly
divergent regions align poorly to the reference and, of course, any sequence not found in the
reference will be missed entirely. Thus, the true extent of diversity within a species is largely
unknown. De-novo genome assemblies and independent annotation can be used to more
accurately estimate the true genomic diversity within a species. We applied this approach using
54 Brachypodium distachyon accessions to create a pan-genome that contains all the diversity
found in the accessions sequenced. Our results indicate that the pan-genome is substantially
larger than the genome of any individual accession, twice as large by some measures. Systematic
comparison of the individual genomes identified a set of core-genes found in all sequenced lines
and a larger set of shell genes present only in some accessions. Our results also characterize the
variability of conserved non-coding sequences among individuals of this species, which we are
correlating with genome-wide expression patterns and gene variability. Together, the core genes,
shell genes and all the non-coding sequences constitute the pan-genome of B.distachyon. Overall,
this work supports a dynamic view of genomes within a species, which is updated with every
new accession studied.
The genetic diversity of a species is the sum of the diversity found in all individuals of that
species. Many studies have attempted to estimate the diversity of a species by resequencing
diverse accessions and aligning the reads to a reference genome. While this approach readily
identifies SNPs and small indels, it underestimates total genomic diversity because highly
divergent regions align poorly to the reference and, of course, any sequence not found in the
reference will be missed entirely. Thus, the true extent of diversity within a species is largely
unknown. De-novo genome assemblies and independent annotation can be used to more
accurately estimate the true genomic diversity within a species. We applied this approach using
54 Brachypodium distachyon accessions to create a pan-genome that contains all the diversity
found in the accessions sequenced. Our results indicate that the pan-genome is substantially
larger than the genome of any individual accession, twice as large by some measures. Systematic
comparison of the individual genomes identified a set of core-genes found in all sequenced lines
and a larger set of shell genes present only in some accessions. Our results also characterize the
variability of conserved non-coding sequences among individuals of this species, which we are
correlating with genome-wide expression patterns and gene variability. Together, the core genes,
shell genes and all the non-coding sequences constitute the pan-genome of B.distachyon. Overall,
this work supports a dynamic view of genomes within a species, which is updated with every
new accession studied.