Direct cloning of sequence tagged microsatellite sites by DNA affinity chromatography

Capturing Darwin's dream

Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream.

Construction of small-insert libraries enriched for short tandem repeat sequences by marker selection

These protocols construct a representative small-insert genomic DNA library in a phagemid vector. First, size-selected DNA fragments are ligated into a phagemid vector. In the second protocol, the resulting small-insert phagemid library is propagated in a bacterial strain combining mutations at the dut and ung loci, which permit incorporation of uracil in place of thymidine during DNA replication. Infection of the phagemid library with M13 helper phage permits recovery of this library as single-stranded DNA (ssDNA). Finally, this uracil-substituted ssDNA is used as a template for primer extension using an oligonucleotide whose sequence corresponds to the STR class of interest [e.g., (GATA)10] as primer. The products of this primer-extension reaction are transformed into an E. coli strain maintaining wild-type genes at the dut and ung loci. Under these conditions, uracil-substituted ssDNA will be restricted from growing by the host-encoded uracil-N-glycosylase, while the primer-extended products are capable of replicating.

Microsatellite hybrid capture technique for simultaneous isolation of various STR markers

The microsatellite hybrid capture technique was designed to enrich simultaneously for various microsatellite repeats from a genomic clone. It is illustrated in this report that different repeat motifs, including polymorphic ones, can be efficiently isolated in a single experiment. In principle, this technique can be applied to any type of genomic clones to facilitate the isolation of informative markers for fine mapping of subchromosomal regions of interest, and for linkage and association studies of candidate genes for which no polymorphic markers are available yet.

A microsatellite marker in Helianthus annuus L

The importance of genetic polymorphism detected by 'microsatellites' is now well established in mammalian genomes. Sequences with a CA repeat, specific to sunflower, Helianthus annuus L., were found by screening a genomic library in M13. After amplification, some polymorphism was detected on these sequences within a sample of cultivars and populations.

The use of microsatellites for genetic analysis of natural populations

Microsatellites, tandemly repeated units of 2 to 5 bp are distributed throughout eukaryotic genomes. Length variation within microsatellites, caused by DNA slippage, can be amplified by PCR and used for DNA profiling. In this paper potential applications and limitations of this technique are discussed. Two case studies for pilot whales (Globicephala melas) and sheep (Ovis aries) exemplify the suitability of microsatellites for analyzing natural populations. Other currently available profiling techniques are compared to microsatellite analysis.

Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences

We describe an efficient method for the construction of small-insert genomic libraries enriched for highly polymorphic, simple sequence repeats. With this approach, libraries in which 40-50% of the members contain (CA)n repeats are produced, representing an approximately 50-fold enrichment over conventional small-insert genomic DNA libraries. Briefly, a genomic library with an average insert size of less than 500 base pairs was constructed in a phagemid vector. Amplification of this library in a dut ung strain of Escherichia coli allowed the recovery of the library as closed circular single-stranded DNA with uracil frequently incorporated in place of thymine. This DNA was used as a template for second-strand DNA synthesis, primed with (CA)n or (TG)n oligonucleotides, at elevated temperatures by a thermostable DNA polymerase. Transformation of this mixture into wild-type E. coli strains resulted in the recovery of primer-extended products as a consequence of the strong genetic selection against single-stranded uracil-containing DNA molecules. In this manner, a library highly enriched for the targeted microsatellite-containing clones was recovered. This approach is widely applicable and can be used to generate marker-selected libraries bearing any simple sequence repeat from cDNAs, whole genomes, single chromosomes, or more restricted chromosomal regions of interest.