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Evolution of beta satellite DNA sequences: evidence for duplication-mediated repeat amplification and spreading
M F Cardone1, L Ballarati, M Ventura
1Dipartimento di Anatomia Patologica e Genetica, Sezione di Genetica, Bari, Italy.
Molecular Biology and Evolution
|June 18, 2004
Summary
The evolutionary history of beta satellite repeats (BSR) in primates began in ape ancestors. BSR amplification and spread occurred in great ape ancestors, with orangutans showing a burst of duplication after divergence from humans.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Genetics
Background:
- Beta satellite repeats (BSR) are repetitive DNA sequences with poorly understood evolutionary histories in primates.
- Previous studies on primate genomics have focused on other repetitive elements, leaving gaps in our understanding of BSR evolution.
Purpose of the Study:
- To investigate the evolutionary history and genomic organization of beta satellite repeats (BSR) in primates.
- To determine the origin and diversification of BSR sequences and their associated duplicons across primate lineages.
Main Methods:
- Comparative genomics analysis of primate genomes, including orangutan, macaque, and gibbon.
- Sequence analysis to identify and characterize BSR sequences and their genomic context.
- Phylogenetic analysis to infer the timing of key evolutionary events.
Main Results:
- BSR sequences in orangutans are organized within large duplicated DNA segments (duplicons) of 60-80 kb, with copy numbers ranging from 70 to 100 per haploid genome.
- The ancestral duplicon appeared in Old World monkeys (25-35 MYA), while the BSR prototype emerged in a gibbon ancestor after the divergence of apes and Old World monkeys (approx. 25 MYA).
- A significant amplification and spread of the BSR-carrying duplicon occurred in orangutans (approx. 18 MYA) after their divergence from the great ape-human lineage, resulting in two variants of BSR length (100 or 170 bp).
Conclusions:
- The evolutionary history of BSR differs from alpha satellite, initiating in ape ancestors with low-copy, non-duplicated sequences.
- BSR amplification and dispersal were facilitated by integration into large duplicons that underwent rapid expansion in great ape ancestors.
- Post-orangutan divergence, BSR acquired a clustered satellite DNA organization, with variants present across hominoid genomes, particularly on acrocentric chromosomes.