Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing comple...

Full description

Saved in:
Bibliographic Details
Published in:Genome research 2022-08, Vol.32 (8), p.1448-1462
Main Authors: Ferrández-Peral, Luis, Zhan, Xiaoyu, Alvarez-Estape, Marina, Chiva, Cristina, Esteller-Cucala, Paula, García-Pérez, Raquel, Julià, Eva, Lizano, Esther, Fornas, Òscar, Sabidó, Eduard, Li, Qiye, Marquès-Bonet, Tomàs, Juan, David, Zhang, Guojie
Format: Article
Language:English
Subjects:
Alternative Splicing
Animal models
Animals
Comparative analysis
Divergence
Evolution, Molecular
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Immune response
Isoforms
Lymphoblastoid cell lines
Macaca mulatta - genetics
Mass spectroscopy
Positive selection
Primates - genetics
Protein Isoforms - genetics
Proteomes
Proteomics
Transcriptome
Transcriptomes
Transcriptomics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
ISSN:1088-9051
1549-5469
1549-5469
DOI:10.1101/gr.276395.121