Upload
ruby-norman
View
217
Download
0
Tags:
Embed Size (px)
Citation preview
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
II. differential expression
2002:low-throughput high-throughput• northern blots• qRT-PCR
Haag et al., 1998
2013:• RNAseq: sequence all mRNAs in sample, count reads
• microarrays (once genes known)
selfing worms have:
• smaller transcriptomes
• less sex-biased expression of remaining genes
Thomas et al. 2012
RNAseqXX vs. XO in 5 Caenorhabditis species
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
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?
• 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?
• A facility for next-gen sequencing exists in 5115 Plant Sciences (5th 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