#high-throughput sequencing

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

Cetaceans (whales, dolphins, and porpoises) have undergone the most dramatic morphological transformation of all mammals, having originated from a clade of terrestrial even-toed ungulates (like cattle, hippopotamuses, pigs, and more) over fifty million years ago. As a result of such an interesting and diverse evolutionary history, cetaceans have long been important and insightful subjects of numerous studies.

Until recently, the higher-level relationships between the cetacean families have taken precedence in research, leaving the systematics and lower-level relationships both under-explored and unresolved. 

New research from Systematic Biology sought to rectify this gap in knowledge by combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, producing the first comprehensive comparative genomic dataset for cetaceans.

In 2006 the world of DNA sequencing was transformed by a company called Solexa introducing the ‘Genome Analyzer’ sequencer. This marked a huge transition from the established Sanger sequencing technology that had been used to sequence the majority of published genomes at that point.

The read lengths produced by the first Genome Analyzer machines were very short, approximately 25 bp. In contrast, Sanger sequencing reads were typically 750–1,000 bp. However, the much reduced length of Solexa reads was offset by the much higher output and lower cost of the technology.

Solexa was swiftly acquired by Illumina and continued technological improvements have led to increases in read length and throughput. Illumina’s popular HiSeq 2500 machines can now produce reads up to 250 bp — an order of magnitude longer than where they started out — and the MiSeq platform goes further still, with read lengths up to 300 bp.

While read lengths produced by Illumina machines are slowly approaching those of the Sanger-sequencing era, other platforms have generated even longer reads. The RS II machine launched by Pacific Biosciences in 2013, produces reads with average lengths of 10–15,000 bp (with some reads exceeding 40,000 bp). Even longer reads have been produced by Oxford Nanopore’s MinION sequencer, with some approaching 100,000 bp (although average read length more closely resemble that of PacBio’s RS II).

Clearly, ever increasing read lengths are an inevitable part of how DNA sequencing technology will evolve…

The new Revolocity system by Complete Genomics does indeed produce reads of just 28 bp! Short is the new long.