1-大数据时代的组学研究【兰州大学生物信息学】

De novo genome
Comparative genomics
• Synteny analysis • Gene family expansion and subtraction • Diversity between species • Genome rearrangement • Chromosome fusion and fission • Ultra conserved elements • Accelerative evolving regions • Phylogenomics
-- James D. Watson
The 1000 Genomes Project
The 1000 Genomes Project
All organisms have a genome
Plants & Animals
Tree of Life
Genome always be the initial understanding of a species
Life is complicated and systematic
中心法则 & Omics
A T C G
基因组 De novo 测序 Re-sequencing Metagenomics Epigenomics
转录组 mRNA lncRNA Small RNA Degradome
蛋白组 Proteome Metabolome
Human Genome Project (HGP)
30亿美元 30亿个碱基对
Biblioteka Baidu
1984 1990
2003
2015
The nations of the world must see that the human genome belongs to the world's people, as opposed to its nations.
Twins
Transcriptome
Proteome & Metabolome
Sequencing Costs and Development
π log-ratio>0.65 and FST >0.17 182 regions (14.5Mb, 0.54% of the genome) 209 genes
Overrepresented GO: Regulation of transmission of nerve impulse (GO:0051969) Arc, ASPA, ATP2B2, MYO6, NTRK2, Rab40c, SNCA, and TG
4,000~3,000 2nd population expansions barley cultivation
Present
Domestication of yak
Human colonization in QTP
Metagenomics
Epigenomics
Expression regulation Genomic imprinting Tissue specific gene expression Diseases related
30 genes involved in Neurogenesis and behavior
Only a few genes subject to physical characteristics and economically significant traits
Early Domestication Stage A trade-off between survival of yaks in a harsh high-altitude environment and
performance under pastoral conditions
Demographic history inferred from SFS
10,000~7,000 1st population expansions
5,200 settle and establish villages (agricultural settlements)
➢ Gene expansion in the yak genome sensory perception energy metabolism
Population genomics
Population structure
Wild yak
Domestic yak
Selection sweeps
“Traditional” VS “Modern” ways
Breakthrough of sequencing technologies
• 1st : Sanger • 2nd : Illumina Solexa; Roche 454; ABI SOLID • 3rd : PacBio SMRT; Oxford Nanopore