ABSTRACT
Illumina sequencing is revolutionizing phylogenomics in the much the same manner as F. Sanger sequencing had spurred the growth of molecular phylogenetics. Although this technology was originally developed for purposes of obtaining whole genome sequences, phylogenomics researchers are primarily using it to target large numbers of specific genomic loci. The Illumina sequencing workflow consists of three basic steps: construction of indexed sequencing libraries; generation of clusters on a flow cell; and sequencing of clusters. For many phylogenomics applications, the starting or “input” deoxyribonucleic acid (DNA) for an Illumina sequencing library usually consists of extracted genomic DNA but it can also be other forms of DNA such as short or long Polymerase chain reaction products. “Blocking DNA mix” consists of different types of DNA that are used to competitively anneal to stretches of repetitive DNA and adapters on pond DNA strands in order to block these sites from catching unwanted library strands.
