Transcriptome innovations in primates revealed by single-molecule long-read sequencing
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Transcriptome innovations in primates revealed by single-molecule long-read sequencing. / 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.
In: Genome Research, Vol. 32, No. 8, 2022, p. 1448-1462.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Transcriptome innovations in primates revealed by single-molecule long-read sequencing
AU - Ferrández-Peral, Luis
AU - Zhan, Xiaoyu
AU - Alvarez-Estape, Marina
AU - Chiva, Cristina
AU - Esteller-Cucala, Paula
AU - García-Pérez, Raquel
AU - Julià, Eva
AU - Lizano, Esther
AU - Fornas, Òscar
AU - Sabidó, Eduard
AU - Li, Qiye
AU - Marquès-Bonet, Tomàs
AU - Juan, David
AU - Zhang, Guojie
N1 - Publisher Copyright: © 2022 Ferrández-Peral et al.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
U2 - 10.1101/gr.276395.121
DO - 10.1101/gr.276395.121
M3 - Journal article
C2 - 35840341
AN - SCOPUS:85137672108
VL - 32
SP - 1448
EP - 1462
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 8
ER -
ID: 322570398