CrowsNest: A Tool to Visualize Synteny Between Plant Genomes Including Recently Published Cereal Genomes of Aegilops tauschii and Hordeum vulgare

CrowsNest has been developed to visualize syntenic relationships between plant genomes, facilitating views on both macro- and micro-syntenic levels.  At first, fully sequenced and assembled reference genomes from Brachypodium distachyon (250 Mb), Oryza sativa (400 Mb) and Sorghum bicolor (700 Mb) were analysed and incorporated. Recently we extended CrowsNest with the anchored physical map of barley (Hordeum vulgare L. spp)[1] (5 Gb), as well as with the published shotgun assembly of Aegilops tauschii [2] (≈5 Gb), both genomes with relatively short sequence contigs but almost complete gene repertoires. Aegilops tauschii represents the progenitor ofthe D-subgenome of bread wheat (Triticum aestivum), with 17 Gb genome size and three similar subgenomeson the way of getting sequenced within the International Wheat Genome Sequencing Consortium (IWGSC) and third amongst the most important crops inthe world. By comparing Aegilops tauschii with barley, a total of 3,576 gene pairswere found where genes are genetically anchored in both genomes and matching each other in a bireciprocal manner. We observe 86.5% (4D-4H) to 93.6% (1D-1H) of bireciprocial matching gene pairs to be located on corresponding chromosomes. This pronounced colinearity suggests that most of the 10,882 additional, but unpositioned gene pairs connected via bireciprocal best hit mightalso be found at the proposed syntenic positions. With various zoom levels and views, CrowsNest faciliates the search for positionally conserved gene loci and blocks between reference and crop plants and provides a basis to explore the gene content and syntenic conservation of repeat-rich cereal genomes in a direct way. The CrowsNest tool (Ae. tauschii-barley instance) can be accessed at http://mips.helmholtz-muenchen.de/plantweb/cgi-bin/mips_cviewer/mips_cgmviewer.pl?tar_genome=Aegilops_tauschii&synteny=ortho&ref_genome=Hordeum_vulgare&ruler=1.

[1]  International Barley Sequencing Consortium, A physical, genetic and functional sequence assembly of the barley genome, 2012
[2]  Luo et al., A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor, 2013