How I spent my summer -- Undergraduate Research Program @ CSHL

By Daniel Burkhart, URP 2014


Daniel Burkhardt, URP 2014

Oryza glaberrima genome sequence provides evidence for its independent domestication.

An international team of researchers published their work on Oryza glaberrima (African rice) genome sequence in the journal Nature Genetics ( The work includes genomics analyses of 20 O. glaberrima and 94 O. barthii accessions, which supported the growing hypothesis that O. glaberrima was domesticated in the Niger river region of Africa. The 33,164 protein coding and 701 tRNA genes were identified in the 314 Mb draft genome of O. glaberrima.

New Plant Reactome pathway projections

Plant Reactome now provides projections for eighteen plant species (nine monocots and nine dicots).

Using curated rice pathways as a reference, Plant Reactome predicts pathways in other plant species on the basis of Compara orthology projections.


The 3,000 Rice Genomes Project

International Rice Research Institute (IRRI), Chinese Agricultural Academy of Sciences (CAAS) and Beijing Genomics Institute (BGI) have come together to sequence the genomes of 3000 rice accessions. A report of this unprecedented sequencing effort and access to the sequence information was recently published in the Journal GigaScience (Jia-Yang Li, Jun Wang, and Robert S Zeigler GigaScience May 2014, 3:8).


Urban rice fields: effective land use under high tension lines in suburban Colombo (photo credit: Aravinda Perera)

Vampires, witchweeds and the Strigolactones

Strigolactones are a class of carotenoid derived compounds. As the most recently described class of plant hormones they are reported to play an ever expanding role in plant development. As a plant hormone, they act like signaling molecules which communicate with other plant hormone systems including auxins, cytokininins and ABA. Equally significant is their role in promoting symbiotic relationships between plants and soil microbes, a key aspect of plant’s mineral nutrition. Interestingly, name “Strigolactone” is derived from this latter role.


Striga (witchweed) parasitizing a maize plant. Source:

Rice gene identifiers in Plant Reactome pathways

Plant Reactome now offers a tab-delimited file containing curated gene product identifiers in rice, grouped by pathway. This data includes IRGSP (RAP/Os), MSU (LOC), and Uniprot identifiers.

Get the data here.

INTERNET OUTAGE on Sunday, June 8 at 11:00 pm EDT

Please be advised that there will be a network upgrade affecting Gramene servers (internet and FTP) on Sunday, June 8th beginning at 11:00PM EDT and concluding at 1:00AM EDT Monday, June 9th.

Plan accordingly so that your work with the Gramene website and services is not affected by the temporary (~2h) internet outage.

Plant Reactome Projection Comparisons

We recently undertook an effort to project our manually curated Plant Reactome Oryza sativa (rice) pathway data onto Zea mays (maize) and Arabidopsis thaliana, and we were curious to compare gene-level projection results derived using both Compara and Inparanoid methodologies.


Breeding bioinformatician open position with SGN

  • Title: Breeding Bioinformatician/Programmer

Gramene database build 41 released

The Gramene Team is pleased to announce its release #41. In collaboration with Ensembl Plants we are providing in this release:


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