3.15 Draft Genome
A draft genome is a collection of sequence reads for a particular species. Draft
genomes are often assembled into contigs and may even be grouped into scaffolds.
3.16 Reference-Quality Genome Sequence
A reference-quality genome sequence is composed of high-quality pseudomolecules
with relatively few gaps between scaffolds. Typically, the DNA used to generate a
reference sequence is from a single individual (see Sect. 2.6 above). Even with
second- and third-generation sequencing techniques, a reference-quality genome is
relatively expensive to produce as efforts must be made to minimize errors in
assembly and fill gaps. However, once a reference-quality genome sequence is
produced, resequencing (see below) can be used to rapidly and cheaply investigate
the molecular nature of genetic diversity.
3.17 De Novo Genome Sequencing
De novo (literally “from new” in Latin) is used to describe a genome sequencing
project for an organism for which there is not a close reference-quality genome
sequence available. Alternatively, it can be used to describe sequencing and assembly of a genome without utilizing an existing reference-quality genome sequence.
This latter form of de novo sequencing is used to test new sequencing techniques and
assembly algorithms (i.e., will our technique be able to produce something comparable to the reference genome sequence?).
⁄
ä
Fig. 7 (continued) have T residues at the position in question). (b) The reads in a contig are used to
produce a consensus sequence for the contig. As highlighted in the gray rectangle, when there is
base discrepancy at a specific position in the contig, the base most commonly found at that position
is included in the consensus sequence (i.e., two of the three reads have a T at the position in
question, and thus the consensus sequence contains a T). (c) Contig consensus sequences, each
represented by a red line, are organized into scaffolds. A number of different physical mapping
techniques (e.g., end sequencing of long molecules, integration of scaffolds with molecular genetic
map data) allow alignment and ordering of contigs in a scaffold. Note that while the scaffold
represents a continuous stretch of DNA, there are gaps of unknown sequence (and sometimes
unknown length) between contigs. (d) A scaffold is shown where red lines represent contig
consensus sequences and gray lines represent gaps between contigs. (e) Physical mapping techniques are used to arrange scaffolds into pseudomolecules that represent whole chromosomes or
linkage groups. Gaps between scaffolds are represented by black lines. Note that centromeric and
telomeric regions are common gap regions in pseudomolecules
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139
A draft genome is a collection of sequence reads for a particular species. Draft
genomes are often assembled into contigs and may even be grouped into scaffolds.
3.16 Reference-Quality Genome Sequence
A reference-quality genome sequence is composed of high-quality pseudomolecules
with relatively few gaps between scaffolds. Typically, the DNA used to generate a
reference sequence is from a single individual (see Sect. 2.6 above). Even with
second- and third-generation sequencing techniques, a reference-quality genome is
relatively expensive to produce as efforts must be made to minimize errors in
assembly and fill gaps. However, once a reference-quality genome sequence is
produced, resequencing (see below) can be used to rapidly and cheaply investigate
the molecular nature of genetic diversity.
3.17 De Novo Genome Sequencing
De novo (literally “from new” in Latin) is used to describe a genome sequencing
project for an organism for which there is not a close reference-quality genome
sequence available. Alternatively, it can be used to describe sequencing and assembly of a genome without utilizing an existing reference-quality genome sequence.
This latter form of de novo sequencing is used to test new sequencing techniques and
assembly algorithms (i.e., will our technique be able to produce something comparable to the reference genome sequence?).
⁄
ä
Fig. 7 (continued) have T residues at the position in question). (b) The reads in a contig are used to
produce a consensus sequence for the contig. As highlighted in the gray rectangle, when there is
base discrepancy at a specific position in the contig, the base most commonly found at that position
is included in the consensus sequence (i.e., two of the three reads have a T at the position in
question, and thus the consensus sequence contains a T). (c) Contig consensus sequences, each
represented by a red line, are organized into scaffolds. A number of different physical mapping
techniques (e.g., end sequencing of long molecules, integration of scaffolds with molecular genetic
map data) allow alignment and ordering of contigs in a scaffold. Note that while the scaffold
represents a continuous stretch of DNA, there are gaps of unknown sequence (and sometimes
unknown length) between contigs. (d) A scaffold is shown where red lines represent contig
consensus sequences and gray lines represent gaps between contigs. (e) Physical mapping techniques are used to arrange scaffolds into pseudomolecules that represent whole chromosomes or
linkage groups. Gaps between scaffolds are represented by black lines. Note that centromeric and
telomeric regions are common gap regions in pseudomolecules
Sequencing Plant Genomes
139