Other Genome Projects

BIOL 473

Summer 2003

Why Other Genomes?

• Proof of principle

• Refinement and advancement of technology

• “Relatively simple” data management

• Models of human disease

• Easy/inexpensive to culture/grow

• Many mutant strains/lines already identified

Importance of Mutant Organismsin Identification of Gene Function

Mutant

Molecular Defect

Gene Function

Vertebrates

Rodent Genome Projects

• ~100 years of genetic research to support genomic findings

• Hundreds of mutant strains, well-characterized genealogies of common strains (esp mice)

• Evolutionary position relative to human:– Close: similar development, physiology & disease

– Divergent: conserved blocks of sequence suggest essential function

Rodent/Human Genome Comparison

• Extensive conservation of nucleotide sequences– Protein-coding regions (genes)– Small, noncoding intergenic regions (SNCIRs)

• Suggests unknown but important function, perhaps regional control of multiple gene expressions

• Extensive conservation of gene order (synteny)– MMU11 syntenic with HSA5 at 1 MB IL region: Perfect

correspondence of order, orientation, and spacing of 23 different genes

– Supports common ancestry– Suggests segmental rearrangement of chromosomes during

evolution

Zebrafish (Danio rerio)• Development rapid and transparent

• Easy to grow

• Dense map of genetic markers

• Many species-specific cell biology tools

– Including human gene transfer

– Including RNAi

– Including organogenesis pathways

• Significant synteny with human and mouse

• >90% similar set of genes with human

Fugu rubripes

PufferfishTetraodon nigroviridis

• Same gene information as humans in 1/8 DNA• Lacks many repeats• Very Small introns (many same ex/in struct)• 400 MY of gene sequence and order conservation• Control regions easy to detect: closer to genes/less nonconserved

intergenic region• 21 chromosomes all smaller than human 21

– Microchromosomes are gene dense

• Important for understanding– Unknown mechanisms of gene expression control– Chromosomal expansion– Function and persistence of “junk DNA”

Other Verts

• Salmon, sticklebacks, cichlids, and other commercial fish• Cats and Dogs

– Common diseases with humans– Important models of morphological variation– Important models of behavioral variation

• Chimpanzee– Mechanisms of pathogen resistance, incl HIV susceptibility– genetic changes crucial for evolution of Homo sapiens

• Agrispecies (cattle, horses; true for crops as well)– Whole genome sequencing prohibitively expensive– Partial genome sequencing and SNPS enhance decades of selective

breeding data• First nutria genome report appeared July 2002!!

– Kass & Doucet: Molecular Phylogeny of the Louisiana Nutria. Proc. LA Acad. Sci. 63:10-24.

The The Founders of Founders of

Nutria Nutria GenomicsGenomics

Why nutria?Why nutria?

Invertebrates

Why?

• Proof-of-principle: sequencing multi-cellular organisms

• Provide understanding of complex organismal functions

• Support decades of genetic research (esp with Drosophila)

Invertebrate Genome ProjectsInvertebrate Genome Projects

Genomic Surprises inDrosophila melanogaster & Caenorhabditis elegans

• Gene Expression anomalies– Ce: leader sequence transplicing

– Ce: polycistronic transcripts

– Dm: high variance in transcript length

– Dm: some distant regulatory sequences & long introns

• 50% more genes in Ce, despite complexity of Dm( # cells, # cell types, morphogenesis)

• Large gene families– Ce: steroid hormone-receptor gene family

– Dm: olfactory receptor gene family

• High conservation of major regulatory and biochemical pathways– some lost to parasitism in Ce

– Some novel to Dm due to complete morphogenesis

• RNAi highly effective in Ce: 90% gene knockout in 2/5 chromosomes

• Models for human disease: 50-60% human disease genes have Ce &Dm orthologs

• Models for drug development– Prozac resistance in Ce; ETOH tolerance in Dm

– No presumption that trait is same, but molecular interaction b/w gene products conserved even when they affect distinct processes

Plants

Arabidopsis thaliana• First plant genome sequenced entirety• 115Mb: about same size as D. melanogaster but 2X

genes (25,500)– Two rounds of whole genome duplication– Extensive chromosome reshuffling– Considerable gene loss after duplication– 1500 tandem arrays repeated genes (2-3 copies @)– Only 11,000 gene families minimum for complex

multicellularity

• 800 nuclear genes of plastid descent– Likely ongoing process– Plastid-targeting signal lost; now function in cyto

• 10% genome is novel miniature repeats (MITEs, MULEs)

Classes of Arabidopsis genes absent/underrepresented in animals:

• Enzymes for cell wall biosynthesis

• Transcellular transport proteins

– Minerals, organics, metabolites, toxins, macros

• Photosynthesis enzymes (rubisco, ETSs)

• Mediators of trophisms (turgor pressure, light, gravity sessility)

• Enzymes and cytochromes for secondary metabolites

• Many R genes (pathogen resistance); interspersed, not clustered

Classes of animal genes absent/underrepresented in Arabidopsis:

Ras G-protein family • Tyrosine kinase receptors • Nuclear steroid receptors

Other Plants Projects & Why?• Projects underway for 50 different species• Rice and Maize: small genomes, economically important

– Many commercial crops plants are polyploid, and genomes are too large to be feasibly sequenced in entirety

– Must rely on comparative genomics to support hybridization data– Rice and Arabidopsis show extensive but complex synteny

• Focus on QTLs rather than Mendelian (single-locus) traits– Resistance, flowering time, tolerance, sugar content, etc.

• Domesticated/wild relationships: maize vs. teosinte• Mutation/morphology relationships: Brassica oleracea

– Cabbage, kale, Brussels sprouts, broccoli, cauliflower, kohlrabi

• Support of classical genetics– Sweet pea, snapdragon

• Support of forestry (Poplar: small genome, easy to grow)– Lumber improvement (lignins, enzymes)– Biomass-biofuel improvment– Bioshperic carbon fixation

• Parent/Ecotype crop comparisons by comparative genomics