Assembling and comparing avian genomes by molecular cytogenetics

There has been a recent explosion in avian genomics. In December 2014 the Beijing Genomics Institute in collaboration with a number of labs worldwide (including Kent) released 48 new de-novo avian genome sequences in a special edition of Science. This has led to a complete re-evaluation of the phylogenetic tree of birds and presents the opportunity to study avian comparative genomics in far more detail than before. Most of these genome sequences however exist only as “scaffolds” i.e. the depth of sequence and length of read produces contiguous fragments of sub-chromosomal size. This impedes insight into overall genome structure, which is particularly challenging, as one of the most interesting biological features of birds is the peculiarity of their karyotype. This project is an on-going effort to map scaffold assemblies to avian chromosomes using a combination of bioinformatics and Fluorescent in situ Hybridization (FISH). This has traditionally been a very time-consuming and costly procedure, however a combination of bioinformatic approaches coupled with novel hardware innovation has deconstructed the FISH protocol and re-invented it as a high throughput, cheaper procedure. Initial work has helped to reconstruct Pigeon and Peregrine Falcon genomes and will ultimately provide insight into various unanswered questions pertaining to avian gross genome rearrangement. These include why the unique overall genomic structure of birds is so evolutionarily conserved, why intra and inter-chromosomal rearrangements happen (e.g. in response to the development of traits such as vocal learning) and what the karyotypes of extinct species such as dinosaurs may have looked like.