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Tools for synteny

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

Data sources

Plant genomes in this database
Species name		Common name	Release version	Gene number	Access	Reference
	Arabidopsis thaliana	thale cress	TAIR 8.0 (Aug. 2008)	26784	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	Project site	--
	Vitis vinifera	grape	Genoscope (Aug. 2007)	37829	Genoscope	Nature
	Oryza sativa	rice	RAP 2.0 (Nov. 2007)	30192	RAP	Nature
	Sorghum bicolor *	sorghum	Sbi 1.4 (Dec. 2007)	34496	JGI	--
In queue
	Glycine max *	soybean	Release 0.1 (Jul. 2008)	--	JGI	--
	Ricinus communis *	castor bean	Release 0.1 (May 2008)	--	TIGR	--
	Brachypodium distachyon *	brachypodium	--	--	USDA	--

* 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.

Click to view the phylogeny

Methods

Identify syntenic blocks

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.

Calculate synonymous substitutions (Ks)

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.

Citations

• 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. [ In press ]

Page last updated: Sep. 01, 2008 Haibao Tang