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Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies
- Source :
- Mol Biol Evol
- Publication Year :
- 2021
- Publisher :
- Oxford University Press (OUP), 2021.
-
Abstract
- LINE-1-mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data mostly relied on detecting discordant mappings of paired-end short reads, or exon junctions contained in short reads. Moreover, there have been few genome-wide comparisons between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate method to identify processed pseudogenes. Our method utilizes long-read assemblies, and more importantly, is able to provide full-length retrocopy sequences as well as flanking regions which are missed by short-read based methods. From 22 human individuals, we pinpointed 40 processed pseudogenes that are not present in the human reference genome GRCh38 and identified 17 pseudogenes that are in GRCh38 but absent from some input individuals. This represents a significantly higher discovery rate than previous reports (39 pseudogenes not in the reference genome out of 939 individuals). We also provided an overview of lineage-specific retrocopies in chimpanzee, gorilla, and orangutan genomes.
- Subjects :
- Pseudogene
Gorilla
Retrotransposon
Genome
Germline
03 medical and health sciences
Exon
0302 clinical medicine
biology.animal
Genetics
Animals
Humans
Molecular Biology
Gene
Discoveries
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
0303 health sciences
Polymorphism, Genetic
biology
Hominidae
Alternative Splicing
Long Interspersed Nucleotide Elements
Genetic Techniques
Evolutionary biology
Pseudogenes
030217 neurology & neurosurgery
Reference genome
Subjects
Details
- ISSN :
- 15371719
- Volume :
- 38
- Database :
- OpenAIRE
- Journal :
- Molecular Biology and Evolution
- Accession number :
- edsair.doi.dedup.....7791eefa5e02fcb97a2947ac2e6149c0