© 2017. All rights reserved.
© 2017. All rights reserved.
Polyploid plants are often larger, more productive and more stress tolerant than their diploid progenitors. Thus, it is not surprising that many highly productive crops are fairly recent allopolyploids (e.g. wheat, strawberry, coffee, cotton). Unfortunately, it is notoriously difficult to assemble high-quality genomes for polyploids due to the presence of highly similar copies of sequences throughout the genome. We recently made an enormous computational breakthrough that allows us to partition sub-genomes of allopolyploid species without any prior information or supervision and with nearly perfect precision and recall (Gordon et al., manuscript in preparation). In fact, this algorithm can inform whether a set of DNA sequences are derived from an allopolyploid in the first place.
Gordon SP, Levy, J, Vogel JP (in preparation) Deciphering complex allopolyploid genomes with unsupervised learning algorithms. Genome Biology
Gordon SP, Levy J, Tartaglio V, Session A, Jenkins J, Shu S, Schmutz J, Barry K, Catalan P, Contreras B, Hasterok R, Doonan J, Mur L, Vinh-Ha D, Chalhoub B, Vogel JP. (in preparation) Snapshots of genome evolution and population dynamics in the allopolyploid grass Brachypodium hybridum. Nature Plants
Dinh-Thi VH, Coriton O, Leclainche I, Arnaud D, Gordon SP, Linc G, Catalan P, Hasterok R, Vogel JP, Jahier J, Chalhoub B (2016) Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PLoS ONE. Dec 9;11(12):e0167171. doi: 10.1371/journal.pone.0167171.
Although not well recognized, individuals and sub-populations of a single species can vary in the presence/absence of genes and other functional sequences (not just alleles). undertook the ambitious goal to determine just how large a eukaryotic pan-genome might be. We de novo assembled and annotated complete genomes for 54 genetically and geographically diverse inbred lines of the model grass Brachypodium distachyon. This work yielded a pan-genome containing nearly twice the number of genes found in any individual genome (Gordon et al., 2017, Nature Communications, in press). Interestingly, of genes that were differentially present among the species-wide pan-genome, many were present in all sampled individuals of certain sub-populations and may be important for adaption to local geographic conditions as well as contributing to the population structure itself.
Currently we are developing PanHipMer to support pan-genomics analyses involving thousands of genomes. To achieve this, we are incorporating annotation and comparative genomics in the assembly process.
Sancho R, Cantalapiedra C, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. (2017) Comparative genomics and phylogenomics of Brachypodium plastomes: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist Early Access
Gordon SP, Contreras-Moreira B, Woods DP, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin A, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Juenger TE, Amasino R, Caicedo AL, Goodstein D, Davidson P, Mur L, Figueroa M, Freeling M, Catalan P, Vogel JP (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications. doi:10.1038/s41467-017-02292-8
Woods D, Bednarek R, Bouche F, Gordon S, Vogel JP, Garvin DF, Amasino RM. (2016) Genetic architecture of flowering-time variation in Brachypodium distachyon. Plant Physiology, Oct;10.1104/pp.16.01178
Gordon SP, Contreras-Moreira B, Woods DP, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin A, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Juenger TE, Amasino R, Caicedo AL, Goodstein D, Davidson P, Mur L, Figueroa M, Freeling M, Catalan P, Vogel JP (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications. doi:10.1038/s41467-017-02292-8
Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CMK, Mannhaupt G, Güldener U, Kahmann R, Djamei A (2016) A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife, Nov;10.7554/eLife.20522
Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin D, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel J. (2014) Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines. Plant Journal, Aug;79(3)
Annual versus perennial growth of plants is a complex trait that has presumably co-evolved with other functional characteristics of an organism in response to a particular environment. The genetic determinants of annual versus perennial life history strategy are largely unknown.
My work developing resources for Brachypodium sylvaticum led to an approved FY2017 JGI CSP grant to sequence many additional annual and perennial species within the genus. The strategy is to use the fact that annual/perennial transitions have occurred at multiple nodes in the tree of this genus and identify candidate genetic correlates common to those events but not found at other speciation events. I plan to continue to collaborate on this project and may pursue other funding.
Gordon SP, Jenkins J, Shu S, Schmutz J, Barry K, Catalan P, Contreras B, Vogel JP. (in preparation) Evolutionary transition from annual to perennial life history in the temperate grass Brachypodium sylvaticum. Molecular Biology and Evolution
Figueroa M, Gordon SP, Garvin DF, Glover-Cutter K, Filichkin SA, Alderman S, Martin R, Vogel JP, Mockler TC, Pfender W (in preparation) A comparative transcriptome study in Brachypodium distachyon to define defense responses to Puccinia graminis formae speciales. BMC Plant Biology
Hsia M, Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams T, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker J, Gu Y, Vogel JP. (2017) High throughput sequencing and functional validation of the JGI Brachypodium distachyon T-DNA Resource. Plant Journal. Apr 22. doi: 10.1111/tpj.13582.
Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, Zhao Z, Kang D, Underwood J, Grigoriev IV, Figueroa M, Schilling JS, Chen F, Wang Z. (2015) Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing. PLoS ONE, July;10(7)