There is a wave of crop reference genomes being generated making it possible to improve navigation of important gene traits for crop improvement. A highly regarded approach toward assessing such traits is through the use of a pan-genome perspective for the genomes. Already there are over 100 reference genomes covering all the cereals: some are included here. For the cereals, genomes generally range in size from 6Gb to 15Gb in size each, depending on ploidy. Model genomes, such as Brachypodium spp. are smaller. Pan-genomes as a resource can begin the journey for evolutionary studies, tracking down individual traits, detecting genome variation by way of structure, tracking integrity of metabolic pathways, as well as leading to other studies in genomics, proteomics, and metabolomics. As many fully sequenced crop genomes quickly appear and multiply, the need for developing annotation pipelines for surveying pan-genomes and connecting them to traits and phenotypes in studied crop systems is imperative to secure our food future.
Here are some links to pangenome studies:
Available:
Under construction:
Publications:
- A genome : Hanin et al. 2023. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 620:830-838
- B genome : Avni et al. 2022. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement. Plant J. 110:179-192.
- D genome : Luo et al. 2017. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498-502
General Pan-Genome Data Resources for Cereals
The PanOat Sequencing Project
Simplified Overview of PanGenome Studies
As these studies evolve, more information will be populated at this location.
