Improved strategies for sequencing complex genomes using high throughput sequencing technologies

Method for determining a genome sequence comprising the steps of: (a) providing a first subset of the genome by digesting the genome with at least one first restriction endonuclease to provide restriction fragments; (B) performing ligating at least one adapter with the restriction fragments of the first subset to provide a first set of restriction fragments ligated to the adapter; (C) selectively amplifying the first set of restriction fragments ligated to the adapter using a first primer combination wherein at least a first primer contains a section complementary to the adapter and a part of the recognition sequence of the restriction endonuclease and further it is containing a selected at the 3 'first sequence' of the primer sequence, comprising the first sequence selected from 0 and 10 nucleotides selective, to provide a first subset of amplified ligated restriction fragments adapter; (D) repeating step (c) with at least one second and / or one or more additional primer combinations wherein the primer contains a different additional sequence selected second and / or at its 3 'containing the same number of selective nucleotides, to provide additional fragments amplified adapter-ligated restriction a second subassemblies and / or; (E) fragmenting each of the additional fragments amplified adapter-ligated restriction subassemblies first, second and / or for generating libraries of additional and / or sequencing the first, second; (F) determining at least part of the nucleotide sequences of at least part of the fragments contained in each of the first and / or additional libraries, second; (G) aligning the sequence of the fragments in each of the first additional libraries, second and / or to generate contigs of the amplified ligated restriction fragments adapter obtained representing dispersed fractions of the genome; (H) repeating steps (a) - (g) for at least a second restriction endonuclease and / or additional; (I) aligning contigs obtained in steps (g) and (h) for each additional restriction endonucleases second and / or to provide a genome sequence.