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Cats and Dogs

by
Cindy Lawley
| Jan 13, 2014

International Plant & Animal Genome (PAG) XXII has officially started and I am already exhausted. There were two full days of exciting species-specific talks before the official opening, and my inner "Energizer bunny" stepped up to the plate! Inevitably I had a talk in one session (the domestication of the tomato) and I desperately wanted to see another talk in another session (alternative splicing in Brassica napus) at the same time. And traversing the gauntlet between sessions without seeing six people I desperately want to talk to is absolutely impossible. I love it!  Here are some highlights from my meeting experience thus far.

On Friday there was the AgENCODE project, which included a presentation by Ewan Birney that provided my favorite analogy at the moment. He highlighted how important consortia and collaborations are in the current funding environment. Individuals (in this case, researchers) tend to be trained with a "cat" mentality: Cats walk alone, independent and proud. The current funding environment and opportunities for partnership with new technologies require a "dog" mentality: Dogs hunt in packs to bring down their prey. The entire AgENCODE session was well organized and Illumina was proud to be a sponsor. We look forward to working with various animal species communities to drive improvements in genome assembly, RNA-Seq, DNaseI Seq, Hi-C, bisulfite sequencing, methyl-seq, and more that will be pivotal to fuel the next revolution in animal genomics. 

Saturday was a whirlwind. In the buffalo genome session, I discussed tools for supporting marker-assisted selection methods now and in the future. The presentation included array methods as well as preliminary data from a study in collaboration with Parco Tecnologico Padano’s Daniela Lamartino] using genotyping by sequencing (GBS) with the HiSeq System. After that I tried (unsuccessfully) to get into the Brassica session (it was packed, like pushing-the-limits-of-the-fire-code packed). I saw about 20 seconds of Dave Edwards's talk while I navigated from one door to the other (blocking others’ view on my way, sorry all!), and he seemed engaging and informative, as usual. 

The afternoon saw me at Nick Tinker's talk where he presented on using GBS with the oat genome in collaboration with Jesse Poland from USDA. Nick was a great speaker and co-coordinator of the oat session. He announced an award of appreciation for the wonderfully disruptive (in a good way) impact of Eric Jackson to the entire oat-breeding community. From there, I headed to the conservation genetics session, where I heard talks on the poplar tree, rainbow trout, and condor. The condor presentation was co-authored by Stephan Schuster (Penn State) and the San Diego Zoo's Oliver Ryder (among others). This project included sequencing with > 80× coverage using paired-end reads and 3× coverage using synthetic long reads (even at just 3× coverage, the assembly noticeably improved). The assembly will be an important reference for efforts seeking to maximize diversity in the condor population. The day wrapped with the Canadian Genome Centres reception, which had a phenomenal attendance. It was delightful to celebrate the impact these institutions have had on improving access to genomic tools for Canadian researchers.

Sunday was another full day. There were animal talks in the bovine, sheep, and goat session about everything from the 1,000 bull genomes project to the microbiome of gut rumen for predicting greenhouse gas impacts (wow, right?). I was sad to have missed the update on the equine genome assembly EquCab3 and hope to catch up with Jim Reecy and Ted Kalbfleisch on the exciting annotation updates. So bummed that I also missed the sessions about forest trees—so many great talks, so little time! My favorite talk of Sunday—I admit that I am biased—was the wonderfully crafted presentation by Amanda Hulse on the Cotton SNP Chip we developed in collaboration with many institutions, including Texas Agrilife Research, the Commonwealth Scientific and Industrial Research Organisation (CSIRO), UC Davis, Brigham Young University, CIRAD, Dow Agrosciences, and several other thought leaders in the cotton genotyping community who were instrumental in driving that effort. It was a highlight of my year to work with this group and successfully build this important tool. The chip targets intraspecific SNPs (Gossypium hirsutum), but includes 20% of interspecific SNPs that will be key to driving new discoveries for introgression and crossing into the commercial lines. I look forward to seeing updates from this community as their data start rolling in! The day was wrapped up nicely by Ewan Birney's presentation in the plenary and the opening of the booths, where I was able to connect with dear friends and collaborators.  

I hope your PAG experience is going as well as mine. Keep your ear to the ground for exciting updates from the Illumina workshop on Tuesday, January 14 at 4:00 p.m. in the Golden West Ballroom.  See you on Twitter (@taylorlawley) if I don't see you in person!


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