Evolution of Genomic Oddities

Explore the fascinating world of avian genomics in this comprehensive lecture on the evolution of genomic oddities in birds. Delve into three intriguing stories about transposons, satellites, and germline/soma genome differences. Discover the challenges of whole genome sequencing and learn how to resolve assembly gaps in these complex genetic puzzles. Examine the unique characteristics of sex chromosomes, including the low collinearity and abundance of endogenous retroviruses in W chromosomes. Investigate the elusive nature of centromeres and their shifts across songbird species. Uncover the surprising revelation that not all cells contain the same genome, exploring programmed DNA elimination and the germline-restricted chromosome (GRC). Gain insights into tissue-specific linked-read sequencing, gene enrichment patterns, and the expression of the GRC in adult gonads. Conclude with an exploration of evolutionary strata on the GRC and its potential emergence in the passerine ancestor, leaving you with thought-provoking take-home messages and future research directions in avian genomics.

Intro
Evolution of genomic oddities: Making sense of transposons, satellites, and germline/soma genome differences in birds
Bird genomes: not much going on?
Three stories about genomic oddities
Whole genome sequence: (still) impossible
Genomics: a big and messy puzzle
How to resolve assembly gaps
Genomes: microcosms of repeats
Sex chromosome differentiation
Making a third-generation assembly
Low collinearity of W chromosomes...
with lots of endogenous retroviruses!
Are W chromosomes toxic like the Y?
Centromeres are often unassemblable...
but can be located in assemblies...
if looking for satellite repeat arrays
Centromere shifts across songbirds
Not so stable chromosomes after all?
Not all cells contain the same genome
Programmed DNA elimination
The germline-restricted chromosome...
Previous work: 18 kb of GRC sequenced
Tissue-specific linked-read sequencing
No enrichment in repetitive elements...
but enrichment in high-copy #genes
The GRC is expressed in adult gonads...
Evolutionary strata on the GRC
Emergence in the passerine ancestor?
Take-home messages part III
Future plans: Why does the GRC exist?
Final thoughts
Acknowledgments