The hidden structural variability in avian genomes

• Structural variants (SVs) are DNA mutations that can have relevant effects at the micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered especially in complex repetitive regions. In this study, we used a combination of long-read and linked-read genome assemblies to explore the occurrence of insertions and deletions across the chromosomes of 14 species birds-of-paradise and two species of estrildid finches. The species sampling encompasses all genera of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. Interestingly, we found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.

Ämnesord

NATURVETENSKAP  -- Biologi -- Evolutionsbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Evolutionary Biology (hsv//eng)

Nyckelord

sex chromosome

avian genomics

deletion

insertion

structural variant

satellite DNA

transposable element

endogenous retrovirus

solo LTR

full-length LTR

Publikations- och innehållstyp

vet (ämneskategori)

ovr (ämneskategori)