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正 Evergreen Fagaceae is a diverse and ecological dominant group in tropical Southeast Asia. They are often used in the pollen record to indicate cooler wet climates in the past and their current distribution indicates that they cannot tolerate seasonal climates For these reasons, the family is a good model group for the historical distribution of evergreen tropical forests in Southeast Asia and the future response of these trees in global climate change. Additionally, the evolution of fruit morphology is under strong selection pressure from seed predation and dispersal, including the repeated convergent evolution of a novel fruit type. Hence, to study the evolution and population dynamics of tropical forest trees, as well as elucidating clues of historical biogeography and the resulted climate change in Southeast Asia and Indochina, we have performed whole-genome shotgun sequencing of 11 species across the Fagaceae family (8 species of Lithocarpus, 2 species of Castanopsis and 1 species of Trigonobalanus) on the Solexa Illumina platform. We evaluated several de novo assembly strategies, given different amounts of data. We explored the classification of the resulting de novo contigs in terms of functional, repetitive elements, and informativeness for comparative ecological and evolutionary analysis.