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Assessment and improvement of Indian‐origin rhesus macaque and M auritian‐origin cynomolgus macaque genome annotations using deep transcriptome sequencing data
Author(s) -
Peng Xinxia,
Pipes Lenore,
Xiong Hao,
Green Richard R.,
Jones Daniel C.,
Ruzzo Walter L.,
Schroth Gary P.,
Mason Christopher E.,
Palermo Robert E.,
Katze Michael G.
Publication year - 2014
Publication title -
journal of medical primatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.31
H-Index - 42
eISSN - 1600-0684
pISSN - 0047-2565
DOI - 10.1111/jmp.12125
Subject(s) - macaque , biology , rhesus macaque , genome , transcriptome , genetics , intergenic region , gene , polyadenylation , deep sequencing , computational biology , rna , gene expression , paleontology
Abstract Background The genome annotations of rhesus ( M acaca mulatta ) and cynomolgus ( M acaca fascicularis ) macaques, two of the most common non‐human primate animal models, are limited. Methods We analyzed large‐scale macaque RNA ‐based next‐generation sequencing ( RNA seq) data to identify un‐annotated macaque transcripts. Results For both macaque species, we uncovered thousands of novel isoforms for annotated genes and thousands of un‐annotated intergenic transcripts enriched with non‐coding RNA s. We also identified thousands of transcript sequences which are partially or completely ‘missing’ from current macaque genome assemblies. We showed that many newly identified transcripts were differentially expressed during SIV infection of rhesus macaques or during Ebola virus infection of cynomolgus macaques. Conclusions For two important macaque species, we uncovered thousands of novel isoforms and un‐annotated intergenic transcripts including coding and non‐coding RNA s, polyadenylated and non‐polyadenylated transcripts. This resource will greatly improve future macaque studies, as demonstrated by their applications in infectious disease studies.