Blast for genomics
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BLAST FOR GENOMICS. Jianxin Ma [email protected] Department of Agronomy Purdue University. Soybean Genome Sequencing Project DOE-JGI Community Sequencing Program Brassica Genome Sequencing Project BGI-Shenzhen, Chinese Academy of Agricultural Sciences. Why transposable elements?.

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Blast for genomics

BLASTFOR GENOMICS

Jianxin Ma

[email protected]

Department of Agronomy

Purdue University


Blast for genomics

Soybean Genome Sequencing Project DOE-JGI Community Sequencing Program Brassica Genome Sequencing Project BGI-Shenzhen, Chinese Academy of Agricultural Sciences


Blast for genomics

Why transposable elements?

  • 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

(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:

~35%

~50%


Blast for genomics

The Landscape of the Soybean Genome

Schmutz et al., 2010, Nature


Blast for genomics

42%

157 families

353 families

16%

58%

Du et al., 2010, BMC Genomics


Blast for genomics

Structure-based analysis

and

Homology-based analysis

(BLAST)


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