Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations

Author:

Shukla Navya12,Shaban Bobbie2,Gallego Romero Irene1234

Affiliation:

1. School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia

2. Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia

3. Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia

4. Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Estonia

Abstract

Abstract Chimpanzees (Pan troglodytes) are a genetically diverse species, consisting of four highly distinct subspecies. As humans’ closest living relative, they have been a key model organism in the study of human evolution, and comparisons of human and chimpanzee transcriptomes have been widely used to characterize differences in gene expression levels that could underlie the phenotypic differences between the two species. However, the subspecies from which these transcriptomic data sets have been derived is not recorded in metadata available in the public NCBI Sequence Read Archive (SRA). Furthermore, labeling of RNA sequencing (RNA-seq) samples is for the most part inconsistent across studies, and the true number of individuals from whom transcriptomic data are available is difficult to ascertain. Thus, we have evaluated genetic diversity at the subspecies and individual level in 486 public RNA-seq samples available in the SRA, spanning the vast majority of public chimpanzee transcriptomic data. Using multiple population genetics approaches, we find that nearly all samples (96.6%) have some degree of Western chimpanzee ancestry. At the individual donor level, we identify multiple samples that have been repeatedly analyzed across different studies and identify a total of 135 genetically distinct individuals within our data, a number that falls to 89 when we exclude likely first- and second-degree relatives. Altogether, our results show that current transcriptomic data from chimpanzees are capturing low levels of genetic diversity relative to what exists in wild chimpanzee populations. These findings provide important context to current comparative transcriptomics research involving chimpanzees.

Publisher

Oxford University Press (OUP)

Subject

Genetics,Ecology, Evolution, Behavior and Systematics

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Generation of chimpanzee induced pluripotent stem cell lines for cross-species comparisons;In Vitro Cellular & Developmental Biology - Animal;2024-02-22

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