Synteny

Synteny is the conserved order of aligned genomic blocks between species. Ensembl Plants includes some synteny analyses generated in house, and some generated by our collaborators Gramene. These methods are summarised below.

Information on current Ensembl Plants synteny data is listed alongside available alignments.

Ensembl synteny method

In-house synteny analyses are calculated from pairwise genome alignments, when both species have a chromosome-level assembly.

This is done in two phases:

1. We search for alignment blocks that are in the same order in the two genomes. Syntenic alignments that are closer than 200 kb are grouped into a synteny block.
2. Groups that are in synteny are linked, provided that no more than two non-syntenic groups are found between them and they are less than 3 Mb apart.

To avoid overly sparse syntenic views, a synteny dataset may be excluded if it has average genomic coverage below a threshold, typically 5%.

For some synteny datasets, analysis parameters may have been tuned to account for differences in the underlying data such as genome size and evolutionary distance.

Gramene synteny method

The Gramene method is based on orthology. For each species combination, the orthologues are assigned a gene index (1..last) depending on order along the chromosome (non-orthologous genes are skipped). DAGchainer software is used to detect collinear genes contained in syntenic blocks, and the coordinates of the syntenic block are derived from the outermost genes within each block. There is no post-processing, so syntenic blocks can sometimes overlap or be nested. The method was used in The B73 Maize Genome: Complexity, Diversity, and Dynamics. Schnable PS et al. 2009. Science 326(5956):1112-1115.