PGDD is a public database to identify and catalog plant genes in terms of intragenome or cross-genome syntenic relationships. Current efforts focus on flowering plants with available whole genome sequences (preferrably assembled pseudomolecules with ordered gene models).

Data sources

Plant genomes in this database (8 genomes)
Species name		Common name	Release version	Gene number	Access	Reference
	Arabidopsis thaliana	thale cress	TAIR 8.0 (Aug. 2008)	26990	TAIR	Nature
	Carica papaya	papaya	EVM (Jul. 2007)	25536	Genbank	Nature
	Populus trichocarpa	poplar	JGI 1.1 (Dec. 2004)	45554	JGI	Science
	Medicago trunculata *	barrel medic	Release 2.0 (Feb. 2008)	38834	UMN	--
	Glycine max *	soybean	Release 1 (Dec. 2008)	75778	JGI	--
	Vitis vinifera	grape	Genoscope (Aug. 2007)	30434	Genoscope	Nature
	Oryza sativa	rice	RAP 2.0 (Nov. 2007)	30192	RAP	Nature
	Sorghum bicolor	sorghum	Sbi 1.4 (Dec. 2007)	34496	JGI	Nature
In queue (4 genomes)
	Arabidopsis lyrata *	lyrate rockcress	Release (Jul. 2008)	--	JGI	--
	Ricinus communis *	castor bean	Release 0.1 (May 2008)	38613	TIGR	--
	Brachypodium distachyon *	purple false brome	Release for 4x-asm	--	OregonState	--
	Zea mays *	corn	Release (Mar. 2009)	--	AGI	--

* Un-published genome data therefore temporarily restricted for downloading. This is in accordance with the understandings in the Fort Lauderdale meeting and NHGRI policy statement for the genome sequencing projects that have not published their major results.

The duplication history of major angiosperm taxa
green circles representing inferred polyploidy events

Methods

We used BLASTP to search for potential anchors (E <1e-5, top 5 matches) between every possible pair of chromosomes in multiple genomes. The homologous pairs are used as the input for MCscan. MCscan is a novel synteny search program that combines the merits of two existent algorithms. The built-in scoring scheme for MCscan is min {-log₁₀E, 50} for every matching gene pairs and -1 for each 10kb distance between anchors, similar to DAGchainer and blocks that have scores >300 were kept. The resulting syntenic chains are evaluated using a procedure in ColinearScan and E-value <1e-10 were used as a significance cutoff.

For homologs inferred from syntenic alignments, we aligned the protein sequences of the gene pairs using CLUSTALW and used the protein alignments to guide CDS alignments by PAL2NAL. Finally, we used Nei-Gojobori method implemented in the PAML package to calculate Ks. An in-house python script is used to pipeline all the calculations. Log-gaussian mixture models are fitted to the Ks distributions using GMM with Bayes Factors.

Number of collinear genes: Total number of genes in genome:
Spread in location A: Spread in location B:

How to cite

• Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M. and Paterson, A.H. (2008) Synteny and Collinearity in Plant Genomes, Science, 320, 486-488. [ Online ]
• Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M. and Paterson, A.H. (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps, Genome Research, 18, 1944-1954. [ Online ]