STRATEGIES FOR SEQUENCING COMPLEX GENOMES USING HIGH THROUGHPUT SEQUENCING TECHNOLOGIES
First Claim
1. A 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) ligating at least one adaptor to the restriction fragments of the first subset to provide a first set of adaptor-ligated restriction fragments;
(c) selectively amplifying the first set of adaptor-ligated restriction fragments using a first primer combination wherein at least a first primer contains a section that is complementary to the adaptor and to part of the recognition sequence of the restriction endonuclease and that further contains a first selected sequence at the 3′
end of the primer sequence, wherein the first selected sequence comprises 1-10 selective nucleotides, to provide a first subset of amplified adaptor-ligated restriction fragments;
(d) repeating step (c) with at least a second and/or further primer combinations wherein the primer contains a different second and/or further selected sequence at its 3′
end that contains the same number of selective nucleotides, to provide for second and/or further subsets of amplified adaptor-ligated restriction fragments;
(e) fragmenting each of the first, second and/or further subsets of amplified adaptor-ligated restriction fragments to generate first, second and/or further sequencing libraries, followed by optional pooling of the libraries;
(f) determine (at least part of) the nucleotide sequence of (at least part of) the fragments contained in each of the first, second and/or further libraries;
(g) aligning the sequence of the fragments in each of the first, second and/or further libraries to generate contigs of the amplified adaptor-ligated restriction fragments derived representing dispersed fractions of the genome;
(h) repeating steps (a)-(g) for at least one second and/or further restriction endonucleases;
(i) aligning the contigs obtained in step (g) and (h) for each of the second and/or further restriction endonucleases to provide for a sequence of the genome.
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Abstract
A method for determining a genome sequence comprising the steps of digesting the genome with at least one first restriction endonuclease, ligating at least one adaptor to the restriction fragments of the first subset, selectively amplifying the first set of adaptor-ligated restriction fragments using a first primer combination wherein at least a first primer contains a first selected sequence at the 3′ end of the primer sequence, comprising 1-10 selective nucleotides, repeating these steps with at least a second primer combinations wherein the primer contains a different second selected sequence, fragmenting each of the subsets of amplified adaptor-ligated restriction fragments to generate sequencing libraries, determine the nucleotide sequence of the fragments, aligning the sequence of the fragments in each of the libraries to generate contigs, repeating these steps for one second and/or further restriction endonucleases, aligning the contigs obtained for each of the second and/or further restriction endonucleases to provide for a sequence of the genome.
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Citations
16 Claims
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1. A method for determining a genome sequence comprising the steps of:
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(a) providing a first subset of the genome by digesting the genome with at least one first restriction endonuclease to provide restriction fragments; (b) ligating at least one adaptor to the restriction fragments of the first subset to provide a first set of adaptor-ligated restriction fragments; (c) selectively amplifying the first set of adaptor-ligated restriction fragments using a first primer combination wherein at least a first primer contains a section that is complementary to the adaptor and to part of the recognition sequence of the restriction endonuclease and that further contains a first selected sequence at the 3′
end of the primer sequence, wherein the first selected sequence comprises 1-10 selective nucleotides, to provide a first subset of amplified adaptor-ligated restriction fragments;(d) repeating step (c) with at least a second and/or further primer combinations wherein the primer contains a different second and/or further selected sequence at its 3′
end that contains the same number of selective nucleotides, to provide for second and/or further subsets of amplified adaptor-ligated restriction fragments;(e) fragmenting each of the first, second and/or further subsets of amplified adaptor-ligated restriction fragments to generate first, second and/or further sequencing libraries, followed by optional pooling of the libraries; (f) determine (at least part of) the nucleotide sequence of (at least part of) the fragments contained in each of the first, second and/or further libraries; (g) aligning the sequence of the fragments in each of the first, second and/or further libraries to generate contigs of the amplified adaptor-ligated restriction fragments derived representing dispersed fractions of the genome; (h) repeating steps (a)-(g) for at least one second and/or further restriction endonucleases; (i) aligning the contigs obtained in step (g) and (h) for each of the second and/or further restriction endonucleases to provide for a sequence of the genome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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Specification