Every genome sequence needs a good map

Reference-assisted chromosome assembly

“…One of the most important advantages of having whole genome sequences is the capacity to understand the evolutionary history of genome organization and structural variation caused by chromosome rearrangements (4)(5)(6)(7). However, the number of animal genomes sequenced by next generation sequencing (NGS) is rapidly outpacing the number of genomes with physical or genetic maps for anchoring the assemblies to chromosomes, which is necessary for elucidating the biological consequences of chromosome rearrangements and for shedding new light on the molecular signatures of human variation and disease mechanisms (8)(9)(10). More large-scale genome sequencing projects are planned using NGS technologies, including the Genome 10K (G10K) and the 5K Insect Genome (i5K) initiatives (11,12).…”

“…The lack of genetic or physical maps for most of the newly sequenced species makes the correct ordering of scaffolds along chromosomes an extremely pressing challenge. As a result, most genomes generated by large-scale projects such as G10K and i5K will lack chromosome assemblies and will be unsuitable to study chromosome evolution (10).…”

“…The larger paired-end libraries or longer sequence reads are more beneficial for correctly assembling repetitive regions. The final output of the assembly algorithms are sequence scaffolds, and the further assembly of the scaffolds to generate chromosome sequences is usually done by integrating with genetic or physical maps (10,22,23). The lack of genetic or physical maps for most of the newly sequenced species makes the correct ordering of scaffolds along chromosomes an extremely pressing challenge.…”

Introduction. Comparative genomics in vertebrates: a role for the platypus

“…This limitation also precludes a confident high resolution analysis of conserved syntenic blocks (stretches of chromosome containing homologous DNA sequences in the in two compared mammal species) in the platypus relative to other mammals (O'Brien et al 1993;Murphy et al 2005;Pontius et al 2007). These deficiencies can be easily remedied by construction of a denser physical map, either FISH, radiation hybrid, or fingerprint based (Lewin et al 2009). …”

Sequence-based physical mapping of complex genomes by whole genome profiling

“…Physical maps are widely used for a range of purposes including positional (map-based) cloning , anchoring chromosomes using fluorescence in situ hybridization (FISH) (Islam-Faridi et al 2002), repeat classification (Cardle et al 2000), draft genome sequence assembly (Sasaki et al 2005), local marker development (van der Vossen et al 2000), and analysis of structural variation in the genome (Kidd et al 2008). Despite advances in next-generation sequencing (NGS) technologies which have accelerated (re)sequencing complete genomes (Hillier et al 2008;Wheeler et al 2008), the need for highquality physical maps remains (Lewin et al 2009). For example, de novo sequencing and assembly of complex genomes containing large regions of repeated sequences will not be easily addressed by NGS alone and require additional procedures to provide anchor points to link sequence contigs and bridge large repeat regions.…”