iPlant Genomics in Education Workshop Genome Exploration in Your Classroom

iPlant Genomics in Education Workshop Major Workshop Concepts: Biology is becoming a “Data Unlimited” science. Genomes are dynamic. Genomes are more than just protein coding genes. DNA sequence is information. Gene annotation adds “meaning” to DNA sequence. Biological concepts like “genes” and “species” continually evolving. DNA barcoding bridges molecular genetics, evolution, ecology.

“BGI, based in China, is the world’s largest genomics research institute, with 167 DNA sequencers producing the equivalent of 2,000 human genomes a day. BGI churns out so much data that it often cannot transmit its results to clients or collaborators over the Internet or other communications lines because that would take weeks. Instead, it sends computer disks containing the data, via FedEx.” The Problem of Big Data in Biology

Human Genome: $2.7 Billion, 13 Years Human Genome: $900, 6 Hours 2012: Oxford Nanopore MiniION 2003: ABI 3730 Sequencer The Problem of Big Data in Biology A decade’s progress

The Problem of Big Data in Biology

The abundance of biological data generated by high- throughput sequencing creates challenges, as well as opportunities: How do scientists share their data and make it publically available? How do scientists extract maximum value from the datasets they generate? How can students and educators (who will need to come to grips with data-intensive biology) be brought into the fold?

The iPlant Collaborative

5-10 year project to develop a computer infrastructure to apply computational thinking to solve biological problems High performance computing Data and data analysis Virtual organization Learning and workforce The iPlant Collaborative

Bringing Genomics into the Classroom Visualization of the Pectobacterium atrosepticum genome

1866 – Mendel publishes work on inheritance 1869 – DNA discovered 1915 – Hunt Morgan describes linkage and recombination 1953 – Structure of DNA described 1956 – Human chromosome number determined 1968 – First gene mapped to autosome 1977 – Dideoxy sequencing 1983 – PCR 1986 – Human Genome Project proposed Bringing Genomics into the Classroom

1993 – First MicroRNAs described 2003 – First ‘Gold Standard’ human genome sequence 2005 – First draft of human haplotype map (HapMap) 2007 – ENCODE project Timeline: Welcome Trust Bringing Genomics into the Classroom

“Essentially, all models are wrong, but some are useful” – George E.P. Box From This…

To This… Bringing Genomics into the Classroom

Majority of genome is transcribed ~50% transposons ~25% protein coding genes/1.3% exons ~23,700 protein coding genes ~160,000 transcripts Average Gene ~ 36,000 bp 7 ~ 300 bp 6 ~5,700 bp 7 alternatively spliced products (95% of genes) RefSeq: ~34,600 “reference sequence” genes (includes pseudogenes, known RNA genes) Bringing Genomics into the Classroom

Using Plants to Explore Genomics

There are a large number of plant genomes available for analysis.

Using Plants to Explore Genomics “Plant genomes range from simple to exceptionally complex” – Richard Chronn, USDA Forest Service It’s this diversity within plant genomes that provides a rich platform for examination of the genome as a phenomenon. Genlisea margaretae 63Mb Paris Japonica 150Gb

Using Plants to Explore Genomics The “weirdness” of plant genomes on your dinner plate Triticum aestivum: allohexaploid Brachypodium Sorghum Oryza Brachypodium

Monocots Dicots Time (million years) Present Oryza (rice) Avena (oats) Hordeum (barley) Triticum (wheat) Setaria (foxtail millet) Pennisetum (pearl millet) Sorghum Zea (maize) Arabidopsis Brachypodium Glycine max (soy) 2,500 Mb 750 Mb 20,000 Mb 270 Mb 430 Mb 145 Mb 1,115 Mb ?? Mb 5,200 Mb >20,000 Mb ?? Mb - Genome duplication event Using Plants to Explore Genomics