Analysis of Biological Functions of Long Tandem Repeats in a Hummingbird Genome Using Next-Generation Mapping Technology

Many plant and animal genomes are difficult to assemble because of the vast amount of long tandem repeat motifs, sometimes spanning several hundred kilobases to multiple megabases. Although repeat motifs can be identified and the amount of repeat material can be approximated by conventional sequencing technologies, it is difficult to assemble them into long contigs, so the exact locations and copy numbers of these repeats remain elusive, especially when the unit length exceeds the read lengths. Without knowing the genomic context or amount of repetitive material, it is impossible to attach biological relevance to them.

Irys^® next-generation mapping technology enables imaging of intact megabase-scale molecules of DNA, so repeats can be spanned and properly placed in the genome assembly. By anchoring next-generation sequencing contigs to genome maps, we can determine the sequence – and potentially the biological function – of the repetitive material.

We present an analysis of repetitive regions in Anna’s hummingbird (Calypte anna). Using the Irys® System, we de novo assembled the genome, including repeat arrays intractable to current NGS methods, identified tandem repeats in BioNano maps using a novel algorithm, anchored Illumina and PacBio contigs to those maps, and investigated sequences within and neighboring those regions. We found a 70 kb repeat contained within a muscle skeletal receptor tyrosine kinase gene, and an 85 kb repeat adjacent to a MAP/microtubule affinity-regulating kinase gene, which suggests that high copy number may correlate with increased muscle activity and glucose metabolism. A public database search suggests that these repetitive elements are hummingbird-specific.