Whole Genome Sequencing &Crop Genetic Breeding

Whole Genome Sequencing &Crop Genetic Breeding

Presentation: Wenhui GaoE-mail: gaowenhui2012@gmail.com

Compeleted genomes in 2013

Outline

1. Introduction to sequencing technology

2. Process of genome sequencing analysis

3. Comprehensive comparison of two cotton genomes

4. Prospect and challenge of genome sequencing

1. Introduction to sequencing technology

(Wendy et al. Molecular Systems Biology. 2013)

Development of sequencing technology

2. Process of genome sequencing analysis

• DNA Isolation & Library construction• Sequencing, assembly, BAC Assessment&

anchoring to chromosome• Repeat sequences mask and annotation• Gene prediction & annotation• Comparative genome & evolution analysis• Species-specific biology analysis• Genome visualization and data submission

Two strategies for Whole Genome Sequencing

Genome assembly

Assessment of assembly accuracy

(The Potato Genome Sequencing Consortium. Nature. 2011)

Pseudochromosome  construction

(Qiang Xu et al. Nat Gen. 2013)

Gene prediction & annotationPrediction• De novo prediction• Homology-based prediction• Transcript-based prediction

(Qiang Xu et al. Nat Gen. 2013)

Annotation• Pfam• KEGG• Gene Ontogy• InterPro• Model organism

(The Tomato Genome Consortium. Nature. 2012)

Comparative genome & evolution analysis

(Kunbo Wang et al. Nat Gen. 2012)

(Jeremy Schmutz et al. Nature. 2013) (Vladimir Shulaev et al. Nat Gen. 2010)

Comparative genome

Whole Genome Duplicate

Phylogenetic tree

Species-specific biology analysis

• Take more attention on the important traits

• Analysis Metabolic pathway• Gene family

–Gene expression patterns–Copy Number Variation

Genome visualization and data submission

3. Comprehensive comparison of two draft genomes of cotton

(Kunbo Wang et al. Nat Gen. 2012)

(Paterson et al. Nature. 2013)

Introduction to cotton

(Hovav et al., PNAS, 2008)

Library preparation

Cotton genome assembly

Assessment of sequence assembly

Anchor to chromosome1369 Markers totally43.8% of the markers (599) were unambiguously located on the assembly73.2%(567.2Mb) was anchored2800 +262 Markers and Vitis vinifera & Theobroma cacao synteny99.95%(761.4Mb) was anchored

Repeat mask and annotation

Retrotransposons: 53%DNA-transposons: 1.5%Satellite tandem: <1%Total: ~56%

Retrotransposons(LTRs): 42.6%DNA-transposons: 4.4%Other repeat: 13%Total: 60%

Gene prediction and annotation

40,976 protein-coding genes

37,505 protein-coding genes77,267 transcripts

Comparative genome & evolution analysis

Biology Stories

In the paper of Paterson, there was a few work about the biology related problems. The main point of this paper was to discuss the evolution about cotton from the whole genome and gene family level.

The evolution in Gossypium

• Evolution from Gr Whole Genome level

• Evolution from specific gene families level

Evolution from Gr Whole Genome

Evolution of functional gene families

• CESA

• CSL

• MYBs

• NBS

CESA

CSL

MYB subgroup 9

NBSGr Chromosome7

Tc Chromosome7

Gr Chromosome13

Genome Visualization

Conclusions about two cotton genomes• Similar process in half part of genome analysis

• Different genome sequencing strategies– Library preparation and sequencing platforms

• Different effect in the final genome– The integrity and accuracy of genome

• Different main points in two papers– China: Whole Genome Duplicate and biology stories– USA : Genome Evolution

Prospect and Challenge of Genome Sequencing

• Need do more work in future WGS• Problems in assembly and alignment (Short reads)• Trends in plant genome sequencing

• Research in polyploidy genome (Homology)– Assembly and alignment– Anchor(Just Using simple Markers is not

enough)– Homologous gene biased expression

Third-generation DNA-sequencing technologies

(John Eid et al. Science. 2009)

Plant genome sequencing

(Catherine et al. Trends in Plant Science. 2011)

Homeolog loss and biased gene expession

Personal viewpoint about Whole Genome Sequencing

• Each step is important in the process of whole genome sequencing

• Make the most of the genome sequencing resource (Not just for one paper)

• The time of polyploidy genome sequencing is coming (challenge and opportunity coexist)

Thank you

(Chen J et al. Nature Communications. 2013)