Lecture #3. How genomes evolve?

• 3.1 Genomic conservation and plant models• 3.2 Genome evolution via du-/triplication• 3.3 Genome evolution via other ways• 3.4 Genomic variations

3.1 Genomic conservation and plant models

• Genomic conservation or genomic synteny:• In classical genetics, synteny describes the

physical co-localization of genetic loci on the same chromosome within an individual or species. Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other

Examples of genomic conservation

• The grass circle

(Gale and Dvos, 1998)

Schnable et al. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science. 326:1112

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(Gui et al. Journal of Integrative Plant Biology, 2010)

• Genomic conservation vs evolutionary distance

• Evolutionary rate

Plant genome models

• Arabidopsis: dicot, 2001• Rice: monocot, 2002

3.3 Genome evolution via du-/triplication

• Genome duplication• Genome triplication

(Plant Genome Duplication Database - University of Georgia)

Genome duplication

• Rice as an example (Case A)

Genome triplication

• tomato

(The Tomato Genome Consortium, 2012, Nature)

双子叶植物经历的一次古老基因组三倍化事件（引自Jaillon等，2007）

（引自Tang 等, 2008）

3.3 Genome evolution via other ways

• Double genome via transposable elements• K. Naito et al., “Unexpected consequences of a sudden and

massive transposon amplification on rice gene expression,” Nature, 461:1130-34, 2009

• A minute plant genome• E. Ibarra-Laclette et al., “Architecture and evolution of

a minute plant genome,” Nature, 498:94-98, 2013

• A carnivorous bladderwort plant Utricularia gibba with 82Mb genome size

U. gibba genome accommodates about 28,500 genes, slightly more than Arabidopsis, papaya, grape

At least three rounds of WGD

Evolution of the minute genome

1. Despite its tiny size, the U. gibba genome accommodates atypical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA, i.e. a small fraction of intergenic DNA 2. with few or no active retrotransposons

A model of genome size reduction and the plant genome sizeevolutionary spectrum

3.4 Genomic variations

• Types of genomic variation• Genomic variations of crops

Genomic variations• SNP: Single Nucleotide Polymorphisms• • Structural variation (SV) is the variation in structure of

an organism's chromosome. It consists of many kinds of variation in the genome of one species, and usually includes microscopic and submicroscopic types, such as deletions, duplications, copy-number variants, insertions, inversions and translocations. Typically a structure variation affects a sequence length about 1Kb to 3Mb, which is larger than SNPs and smaller than chromosome abnormality

• Natural plant populations/Crop populations

Genomic variations in natural population

• Arabidopsis as an example• Wild relatives of crops will be next

investigation targets: • Wild rice: Origin of rice domestication. Huang

et al, 2012, Nature• Wild and semi-wild soybean populations for

gene flow of trangenic crops

Arabidopsis population

• The 1001 Genomes Project (www.1001genomes.org)

• A catalog of Arabidopsis thaliana Genetic Variation

• Level of genomic variation (SNP density): ?

Wild rice population

• Origin of rice domestication. Huang et al, 2012, Nature• 446 diverse O.rufipogon accession

• Level of genomic variation (SNP density) of wild rice:

• Paddy weed: barnyard grass (Echinochloa crus-galli): similar to crops

Genomic variations in crop population

(Qi et al., 2013, Nature Genetics)

Examples

• Inter-cultivar• maize as an examples

• Intra-cultivar• Soybean as an example

Intercultivar variation is so big

• Maize genomic variation

• 35% genomic synteny between two genomes of cultivars

• 2Mb PAV

Annotation of large-effect SNPs

Numbers of PAVs relative to the B73 reference genome

• 296 high-confidence genes in B73 that were missing from at least one the six inbred lines.

• One large deletion between Mo17 and B73: ~2Mb with 24 genes

Intracultivar genomic heterogeneity was observed

• A same phenotype for individuals from a cultivar

• A reference genome of soybean (William 82): Haun et al. Plant Phiso., 2011

The composition and origin of genomic variation among individuals

of the soybean reference cultivar Williams 82

• Haun et al. 2011, Plant Physio.• Williams 82: a Williams×Kingwa BC6F3

generation

SNP genotyping (SNP chip) reveals the parental origins of Williams 82 genetic

heterogeneity

Structural variation (CGH) within regions of heterogeneity between

two Williams 82 individuals

Exome resequencing reveals gene content variation between two

Williams 82 lines

A model for the origin of genomic heterogeneity in two Williams 82

lines

Implications for the Williams 82 and other plant genome sequences• Within regions of genetic heterogeneity, the reference

sequences consist of a mosaic of the Williams and Kingwa haplotypes.

• Researchers investigating comparative studies of soybean that include Williams 82 as a reference genotype must factor in the inherent differences between each Williams 82 individual and the reference genome sequence.

• Similar considerations will need to be made for a variety of comparative methodologies, such as RNA-SEQ data.

• Similar circumstances may apply to the utility of other plant genome sequences