Genome skimming
[1] Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods.
Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.
[1] The plastid genome, or plastome, has been used extensively in identification and evolutionary studies using genome skimming due to its high abundance within plants (~3-5% of cell DNA), small size, simple structure, greater conservation of gene structure than nuclear or mitochondrial genes.
[8][9] Plastids studies have previously been limited by the number of regions that could be assessed in traditional approaches.
Compared to the typical DNA barcode, genome skimming produces plastomes at a tenth of the cost per base.
[5] Recent uses of genome skims of plastomes have allowed greater resolution of phylogenies, higher differentiation of specific groups within taxa, and more accurate estimates of biodiversity.
[9] When targeting plastomes, it is suggested that a minimum final sequencing depth of 30X is achieved for single-copy regions to ensure high-quality assemblies.
[10] The increased publishing of complete mitogenomes allows for inference of robust phylogenies across many taxonomic groups, and it can capture events such as gene rearrangements and positioning of mobile genetic elements.
Using genome skimming to assemble complete mitogenomes, the phylogenetic history and biodiversity of many organisms can be resolved.
Genome skimming, on the other hand, can be used to extract genetic information from preserved species in herbariums and museums, where the DNA is often very degraded, and very little remains.
[15] Genome skimming has been shown to detect the low quantity of DNA from this ethanol-fraction and provide information about the biomass of the specimens in a fraction, the microbiota of outer tissue layers and the gut contents (like prey) released by the vomit reflex.
[15] Thus, genome skimming can provide an additional method of understanding ecology via low copy DNA.
[15] DNA extraction protocols will vary depending on the source of the sample (i.e. plants, animals, etc.).
Hyb-Seq is a new protocol for capturing low-copy nuclear genes that combines target enrichment and genome skimming.
Using the final recruited organellar-associated reads, GetOrganelle conducts a de novo assembly, using SPAdes.
It uses built-in database or user specified reference to extract orthologous sequences from plastid, mitochondrial and nuclear ribosomal regions using a BLAST search.
[37][38] Since the organellar genomes will be high-copy in the cell, in silico genome skimming essentially filters out nuclear sequences, leaving a higher organellar to nuclear sequence ratio for assembly, reducing the complexity of the assembly paradigm.
[1] Other than the current uses listed above, genome skimming has also been applied to other tasks, such as quantifying pollen mixtures,[19] monitoring and conservation of certain populations.
[3] This provides a low-risk avenue for biological inquiry and hypothesis generation without a huge commitment of resources.
[5] The preservation processes in ethanol often damage the genomic DNA, which hinders the success of standard PCR protocols[3] and other amplicon-based approaches.
Library preparation for specific to genome skimming has been shown to work with as low as 37 ng of DNA (0.2 ng/ul), 135-fold less than recommended by Illumina.
[1] A combination of sequencing depth and read type, as well as genomic target (plastome, mitogenome, etc.
