Splitting maize genome

The ancestor of modern maize/corn went through a Whole genome duplication sometime between 5 and 12 million years ago (after the maize and sorghum lineages split). Using the chromosomes of the sorghum genome as an outgroup we can accurately identity which parts of each chromosome are represented by which parts of the maize genome.

The logic used to reconstruct maize chromosome pairs doesn't allow us to assign those chromosomes into two unique pseudo-genomes. Reconstructed chromosomes were assigned to maize1 or maize2 based on the direction of biased gene loss. Maize1 consists of the reconstructed chromosomes from which fewer genes have been lost since the maize whole genome duplication and maize2 of the reconstructed chromosomes from which more genes have been lost (as determined by comparison to the sorghum outgroup). This grouping is useful for comparative analysis, but we can't say that the assignments of pseudo-chromosomes to either maize1 or maize2 represent the actual groupings of those chromosomes in the pre-tetraploidy ancestors of maize. With 10 pairs of pseudo-chromosomes there are 512 possible arrangements.

With that caveat, for each sorghum chromosomes, here are the maize chromosomes we drew pieces from to reconstruct the two copies that existed in the ancestor of maize right after the maize whole genome duplication.

Sorghum Chromosome	Maize 1	Maize 2
1	1	5,9
2	7	2
3	3	8
4	5	4
5	4	2
6	2	10
7	1,6,10	4
8	1,10	3
9	10,6	8
10	9,5	6