b'S T R A T E G Y A featured segment designed to help you in the realm of retail seed sales. Solving the Asian Soybean Rust PuzzleScientists have sequenced the Asian soybean rust genome, but what does that mean for the seed industry? Joe FunkIN SEPTEMBER 2019,was the researchers first sur-an international researchprise. This information could collaboration announcedimply a much larger gene it had successfully assem- complement in the soybean bled a complete reference- rust than in other rust fungi. quality genome sequenceSo far, the numbers of genes of Phakopsora pachyrhizi,reported in rust fungi are the fungal pathogen thatbetween 15,000 and 20,000 causes Asian soybean rustgenes. Researchers second (ASR) which has a devas- surprise was the type of tating impact on soybeangenetic information contained production, an internationallyin the genome.important crop with 380 mil- The pathogens genome is lion tons produced globally.so big and so complex that no Soybean rust poses a threatorganization could individually to U.S. soybean productioncomplete the project. It was and is a crucial challenge forbeyond our capability, so we soybean growers around thedecided to pool our resources world.Soybean rust poses a treat to U.S. and global soybean production. and make everything pub-Asian soybean rust is alicly available, explains van significant challenge for soy- Esse. The genomes large bean growers, says Peter vanof sequences assembled intoCompany of Agriculturalsize hampered progress Esse, leader of the 2Bladeschromosomes. The fungus P.Research (Embrapa), lInstitutuntil KeyGene provided its Group at The Sainsburypachyrhizi has a large, com- National de la Recherchelong-read, high-molecular-Laboratory, Norwich, one ofplex genome. It is composedAgronomique (INRA - France),weight DNA-isolation pro-the collaborators. This refer- of 93% repetitive elements,the German Universitiestocol technology so that we ence level genome assemblya level of complexity thatof Hohenheim and RWTHcould span those repetitive will allow the scientific com- has delayed progress on theAachen, and the Federalsequences and the genome munity to study, in unprec- sequencing of this pathogenUniversity of Viosa (Brazil).assembly. By putting all the edented resolution, thoseand required the latest indata of the partners together, components of the pathogennext-generation sequencingGenomic Surprises we were able to assemble that are critical for causingtechnologies to complete theGoing into the project,a high-quality genome and disease. This is an essentialtask. researchers assumed theyannotate the gene content first step toward the design of The international researchwould be working with afrom which we can learn a lot. transformative control strate- consortium behind this effortfungus that had a smallAll in all, this has been 10 years gies to combat this highlyincludes 11 research and indus- genome similar to other fungiin the making. It is a long story damaging pathogen.try partners. In addition towith around 50 megabase- of learning how complicated High-quality, referenceThe 2Blades Foundation andpairs (50 Mb). Very quickly, itthis genome is. It has taken genomes are differentiatedThe Sainsbury Laboratory,became evident that P. pach- our best bio-informaticians from draft genomes by theirparticipating partners includeyrhizi has a huge genome,and biologists to bring this completeness (a low numberKeyGene, the Joint Genomeperhaps as large as 1000 Mb,together.of gaps), a low number ofInstitute (JGI), Bayer AG,which is as much as 20 timesAs genomic researchers errors and a high percentageSyngenta AG, the Brazilianlarger than anticipated. Thatinitially encountered long 44/ SEEDWORLD.COMJUNE 2020'