BTI researchers share latest research at ag-genomics conference

The offices of data scientists at BTI emptied out earlier this month as a contingent of researchers flew to San Diego for the 25^th annual Plant and Animal Genome Conference.

Genomic researchers from around the world gathered at the meeting to network, consult with colleagues and hear the newest advances in genome sequencing technology and analysis. Many BTI scientists have attended for years and presented their work on agriculturally important plant and insect species. The conference occurred January 14-18.

Bioinformatics researchers led by Associate Professor Lukas Mueller presented a workshop on their Sol Genomic Network (SGN) and Root Tubers & Banana (RTB) Databases, to demonstrate the newest genomic research tools that they have developed for breeders and scientists working with multiple crops – tomato, potato, pepper, cassava, sweet potato and others. As part of this workshop, Hartmut Foerster gave a talk on a collection of databases that capture gene, enzyme and metabolic information for different plant species. Mueller presented a workshop on cassavabase, and visiting scholar Angelot Paterne Agre from the International Institute of Tropical Agriculture gave a talk on yambase—two genomic resources that will accelerate breeding of these two important staple crops.

This year, Mirella Flores, a database programmer in the Mueller lab, presented the latest release of the tomato genome—version 3.0. Many of the gaps in the existing genome sequence have been filled in. The researchers also used a technology called Bionano that helps them to verify that their genome assembly is correct, and to incorporate orphan sequences that had been left out initially. Bioinformatics analyst Prashant Hosmani presented their most recent efforts to annotate the tomato genome, a process that identifies the various genes and assigns them a function.

Coffee drinkers will be interested to hear that Susan Strickler, a bioinformatics consultant and research associate in the Mueller lab, presented her work with the Arabica Coffee Genome Consortium. The group has sequenced Coffea arabica – the high-quality bean that connoisseurs know and love – as well as its parent species, Coffea canephora (which is the cheaper but hardier robusta kind) and the rarely consumed Coffea eugenoides. Though not a coffee drinker herself, Strickler hopes that the genomes will serve as a resource for breeders who want to improve the coffee plant and make it more disease-resistant.

In the insect world, Surya Saha, senior bioinformatics analyst, gave an update on their ongoing efforts to put together a complete genome sequence for the Asian citrus psyllid, which spreads the bacterium that causes citrus greening disease. They used a new technology from 10X Genomics that can sequence the genome of a single tiny psyllid. The resulting sequence is helping them to clarify the existing sequence, which is based on a confusing mix of genomes from 50 to 100 psyllids. He is also working to create a metabolic pathway database for citrus fruits, specifically the orange and clementine, that makes connections between the genes, proteins and metabolites.

Several other BTI researchers will also presented their work at the conference. New faculty member Fay-Wei Li highlighted new findings from his work sequencing several fern genomes, which he will use to provide a broader view of fern evolution. Kelly Robbins of the Genomic & Open-source Breeding Informatics Initiative (GOBII), a Cornell-led project in collaboration with BTI and the USDA, gave an overview of the data management system that they are developing for crop breeders. The system will enable researchers to use genomic data to accelerate the breeding of better crops. Additionally, colleagues of the Fei lab presented their work on watermelon domestication and fruit quality.

For more information on work presented at The International Plant & Animal Genome XXV, see their program.