Plenary talk - Chromosomally complete reference genomes for challenging species: overcoming sequencing dropout in bird microchromosomes
- luisamarins19
- Apr 9
- 2 min read
Updated: 10 hours ago
At this month's ERGA Plenary meeting, taking place on Monday, April 28 at 15:00 CEST, Dr. Thomas Mathers will present his work on a Tree of Life pilot project focused on improving reference genome assemblies for challenging species, along with new insights from complete bird microchromosome assemblies.
More details can be found below.
Watch the recorded talk:
Abstract
Chromosomally complete reference genomes for challenging species: overcoming sequencing dropout in bird microchromosomes
Large genome assembly projects aim to generate chromosomally complete reference genomes across the tree of life. Typically, these projects rely on PacBio HiFi long-read sequencing and HiC to deliver reference genomes at scale. This approach results in high-quality genome assemblies that meet or exceed gold standard metrics for most lineages. However, some species are recalcitrant to assembly and challenges remain to generate high-quality genome assemblies for all taxa. Within vertebrates, birds present a substantial assembly challenge due to the presence of tiny, hard to assemble, microchromosomes. These chromosomes have distinct genetic and epigenetic features and are highly fragmented in PacBio HiFi de novo assemblies, to the extent that in many cases the full complement of chromosomes cannot be identified. In this talk, I present results from a Tree of Life pilot project to improve the reference genomes of 20 bird species using Oxford Nanopore long-read sequencing. We find that using PacBio HiFi reads for de novo assembly results in up to 70% missing gene content on the 10 smallest bird chromosomes due to sequence coverage dropout. I will discuss the possible causes for this sequence dropout and highlight new insights from complete microchromosome assemblies.
Speaker's Bio
Thomas Mathers
Tom is a former BBSRC Future Leader (Discovery) Fellow at the John Innes Centre where he studied the evolutionary genomics of crop pest host range and is currently a Senior Computer Biologist at the Welcome Sanger Institute working on the Tree of Life Project. At Sanger, Tom carries out genome curation, develops tools to support curation efforts and leads projects making use of Tree of Life genomes to improve genome assembly methods and gain insights into basic biology through genome analysis. Recent projects include assembly and comparative analysis of bird microchromosomes, identification and evolution of supernumerary B chromosomes and sex chromosome turnover in flies.
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