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Plant and Animal Genomics Conference XXII, San Diego, USA 10th – 15th January 2014.
Over the last 22 years, PAG always took place in the same location in San Diego (California, USA) during the first half of January. In many ways PAG is a superlative with over 2,500 academics attending, with the ability to see up to 54 oral presentations per day for five days, and around 800 scientific posters. Not to mention the brilliant weather at this superb location in southern California.
For the first time, a really useful smartphone app was released that helped to plan your day and navigate around the vast diversity of topics.
Of great importance for our field were the two workshops on the interaction of plants with microbes, pathogens and pests. Talks concentrated on sequencing and assembly efforts of several pathogenic rust fungi as well as oomycetes.
Beat Keller for example highlighted the draft genomes of the powdery mildews of barley and wheat. Both genomes seem difficult to assemble with 90% repeat content. So far, over 550 secreted proteins were predicted. Numerous other talks in diverse sessions highlighted also genomics based improvements in plant disease resistance breeding. Of interest to me was the presentation of the chili pepper genome by Prof. Doil Choi. The genome of this diploid Solanaceae is between 3. 2 and 5. 6 Gb large with 74% repeat content.
Currently 733 NB-LRR like disease resistance genes were predicted – a number that is very similar to potato. Caroline Dean of the John Innes Center in Norwich, highlighted results from her lab that identified the epigenetic regulation that underlies vernalisation of Arabidopsis plants for flowering.
Highlights were also the plenary lectures taking place over three days, spear headed by Ewan Birney from EMBL-EBI. Ewan explained the importance of the institution he is president of, for the genomics community but also all other fields where sequence analysis is used. In his lecture, he talked about a project that he planned several years ago to store information as DNA. The biggest problems with this approach however are the high costs and the short length of synthesized DNA, but also indexing solutions are necessary to facilitate identifying the right DNA sequence that encodes your file of interest.
Groundbreaking news in sequencing or assembly technologies were however not presented this year, only upgrades of existing platforms. PacBio presented results from their last released chemistry, which allows for an average length of 8kb and a maximum of over 30kb.
During 2014 a new chemistry will be released that will increase these numbers further to an average length up to 12kb. A great success could be the assembler for diploid genomes that is supposed to be released later this year.
The friendly atmosphere on site makes PAG a great place to meet with old friends, collaborators and to make new friends. This was my first visit to PAG, but definitely not the last. I want to thank BSPP for the financial help towards the travel costs.
Florian Jupe The Sainsbury Laboratory, Norwich.