1. I. defining genomes and their contents 2002: Sanger sequencing technology (few, long reads) EST projects (random cDNA clones) cloned gDNA (cosmids, fosmids, plasmids lambda phage) initial sequencing of human genome: ~15 years, 100’s of people, $3,000,000,000 2012: Next-generation sequencing technology (huge numbers of short reads) de novo transcriptome assembly massively parallel whole-genome shotgun re-sequence human genome (with poor assembly): one week, ~ 2 people, ~$3,000 (and falling…) McGrath, 2007

2. II. differential expression 2002: low-throughputhigh-throughput northern blots qRT-PCR Haag et al., 1998 2013: RNAseq:sequence all mRNAs in sample, count reads microarrays (once genes known)

3. selfing worms have: smaller transcriptomes less sex-biased expression of remaining genes Thomas et al. 2012 RNAseq XX vs. XO in 5 Caenorhabditis species

4. III. genotype-phenotype association & evolutionary history 2002: identify markers (microsatellites, SNPs, RFLP) build recombination map map traits (induced or natural) to ever-smaller interval 2012: localize induced or clinical mutants by resequencing GWAS/QTL without map or pre-existing markers (even in wild populations) Implications for: medicine cell/developmental biology evolution ecological

5. Sequence data should no longer be regarded as representative samples of a vast and unknowable whole. We are now in the era of the finite (and affordable) genome. How big can you think?

6. Which regions of the genome are selected when an aphid switches host, when a fish evolves to live in caves, or when a marmot experiences climate change? Which transcripts increase in the cortex as a mouse develops ocular dominance, or in an annelid or a lamprey nerve cord as it regenerates? Does Silene have X-dosage compensation between the sexes? [just published!] Do chytrid-resistant frogs or drug-resistant Trypanosomes have any gene variants in common? What is the recombination map for a bat, a penguin, or a Panamanian fig tree? Exactly how many new mutations arise in a single generation of Arabidopsis?

7. A facility for next-gen sequencing exists in 5115 Plant Sciences (5 th Floor) Managed by Suwei (“Sue”) Zhao, with assistance from Kongyi (“Candy”) Jiang Suwei (R), Kongyi (L) (with Jerry Regier) http://www.ibbr.umd.edu/facilities/sequencing