James Schnable is a graduate student in the Freeling Lab. His research focuses on comparative grass genomics and the fate of genes following whole genome duplications.
- in progress PhD, Plant Biology, University of California-Berkeley (Advisor Michael Freeling) 2008-present
- BA, Biology (Focuses in Genetics and Plant Biology), Cornell University 2004-2008
I study what makes the two subgenomes within ancient tetraploid species such as maize different from each other. By taking advantage of the huge datasets that are now routinely generated by research groups using 2nd generation sequencers, I am studying how homeologs (duplicate genes created by a whole genome duplication, also known as ohnologs) on the two subgenomes of maize behave differently.
In addition to having lots of well characterized mutants and a relative abundance of RNA-seq data, studying the evolutionary and genomic consequences of polyploidy in maize also benefits from the fact that the grass family (Poaceae), of which maize is a member, are represented by the most species with sequenced genomes of any plant family (which only makes sense when you consider the crucial roles grasses play in both agriculture and ecology). Using comparative genomics to identify and compare orthologous regions of different grass genomes, we can identify where duplicate genes were completely or partially removed from the maize genome following its ancient whole genome duplication, as well as conserved noncoding sequences thought to be involved in regulating the expression of genes.
In the long term, my goal is to test the hypothesis that duplicated transcription factors from the maize whole genome duplication underly the emergence of two separate and morphologically distinct inflorescences in maize -- the ear and tassel shown on the left and right sides of the attached image-- when most other members of the Andropogoneae (the grass tribe to which maize, sorghum, and sugar cane belong to) have only a single style of inflorescence bisexual flowers as seen it the sorghum head in the center of the attached image. The comparison of maize and sorghum inflorescences on the right is a Creative Commons Licensed Image which was the featured image of the PLoS Biology June issue and came from a paper published by myself and other members of the Freeling lab describing fractionation -- the loss of duplicate gene copies following a whole genome -- in the maize genome. See the image in its original context.
- Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. (2012) Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current Opinion in Plant Biology DOI: 10.1016/j.pbi.2012.01.015
- Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant GC, Wang X, Freeling M, Pires JC. (2012) Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics DOI: 10.1534/genetics.111.137349
- Schnable JC, Freeling M, Lyons E. (2012) Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution DOI: 10.1093/gbe/evs009
- Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, and Jiang J. (2011) High-resolution mapping of open chromatin in the rice genome. Genome Research DOI: 10.1101/gr.131342.111
- Eichten SR,* Swanson-Wagner RA,* Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. (2011) Heritable epigenetic variation among maize inbreds. PLoS Genetics DOI: 10.1371/journal.pgen.1002372
- Schnable JC, Lyons E. (2011) Comparative genomics with maize and other grass: from genes to genomes. Maydica 56(2) 183-200 (pdf link)
- Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics DOI: 10.1186/1471-2105-12-102
- Schnable JC, Pedersen BS, Subramaniam S, Freeling M. (2011) Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses. Frontiers in Plant Science DOI: 10.3389/fpls.2011.00002
- Schnable JC, Freeling M. (2011) Genes identified by visible mutant phenotypes show increased bias towards one of two maize subgenomes. PLoS One DOI: 10.1371/journal.pone.0017855
- Schnable JC, Springer NM, Freeling M. (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.110136810
- Woodhouse MR,* Schnable JC,* Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology DOI: 10.1371/journal.pbio.100040
- The International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature DOI: 10.1038/nature0874