BLASTBLAST FOR GENOMICS FOR GENOMICS

Jianxin Mamaj@purdue.edu

Department of AgronomyPurdue University

Soybean Genome Sequencing Project Soybean Genome Sequencing Project DOE-JGI Community Sequencing Program DOE-JGI Community Sequencing Program

Brassica Genome Sequencing Project Brassica Genome Sequencing Project BGI-Shenzhen, Chinese Academy of Agricultural BGI-Shenzhen, Chinese Academy of Agricultural Sciences Sciences

Transposable elements (TEs), popularly called “jumping genes” are sequences of DNA that can move around to different chromosomal positions in a cell.

First TEs were discovered in maize in 1948 by Barbara McClintock

Awarded the Nobel Prize in 1983

Why transposable elements?

(1902-1992)

TEs make up a large fraction of genome sizes in most higher organisms:

TEs were often referred to be “molecular junk”, but are now recognized as important, even crucial parts of the blueprints of plants and animals:

~50% ~35%

Schmutz et al., 2010, Nature

The Landscape of the Soybean GenomeThe Landscape of the Soybean Genome

157 families

353 families

42%

16%

58%

Du et al., 2010, BMC Genomics

Structure-based analysis

and

Homology-based analysis

Structure-based analysis

and

Homology-based analysis

(BLAST)(BLAST)