2006 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Cold Spring Harbor Laboratory. Additional details of this research can be found in the report of the parent project 1907-21000-023-00D "Comparative Genomic Analyses, Bioinformatics and Resource Development for Cereal Genomes." This work focuses on extending resources and continuing to develop new resources to increase our understanding of complex genome organization of cereals and develop methods to sequence large plant genomes. In the past year, sequence was generated and utilized in the analysis conducted under a Non-funded Cooperative Agreement between ARS and Cold Spring Harbor Laboratory; ARS project 1907-21000-023-02N entitled "Genomics of Rice, Sorghum and Maize."