Comparative RNA sequencing reveals substantial genetic variation in endangered primates
George H. Perry,Páll Melsted,Páll Melsted,John C. Marioni,Ying Wang,Russell Bainer,Joseph K. Pickrell,Katelyn Michelini,Sarah Zehr,Anne D. Yoder,Matthew Stephens,Jonathan K. Pritchard,Yoav Gilad +12 more
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TLDR
This study sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates, identified patterns of variation that are consistent with the action of positive or directional selection, and found no relationship between genetic diversity and endangered status.Abstract:
Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success.read more
Citations
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Computational and analytical challenges in single-cell transcriptomics
TL;DR: The development of high-throughput RNA sequencing at the single-cell level has already led to profound new discoveries in biology, ranging from the identification of novel cell types to the study of global patterns of stochastic gene expression.
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Detecting natural selection in genomic data.
TL;DR: A comprehensive outline of evolutionary genomics methods is provided, highlighting the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.
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Comparative population genomics in animals uncovers the determinants of genetic diversity
Jonathan Romiguier,Philippe Gayral,Marion Ballenghien,Aurélien Bernard,Vincent Cahais,Anne Chenuil,Ylenia Chiari,Rémy Dernat,Laurent Duret,Nicolas Faivre,Etienne Loire,Joao M. Lourenco,Benoit Nabholz,Camille Roux,Georgia Tsagkogeorga,Alexandra Anh-Thu Weber,Lucy A. Weinert,Khalid Belkhir,Nicolas Bierne,Sylvain Glémin,Nicolas Galtier +20 more
TL;DR: It is shown that the diversity of a species is predictable, and is determined in the first place by its ecological strategy, and demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations.
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Hans Ellegren,Nicolas Galtier +1 more
TL;DR: Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' — the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels.
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Comparative studies of gene expression and the evolution of gene regulation.
TL;DR: Comparative studies in primates and how they are complemented by studies in model organisms are focused on to link gene regulatory changes to adaptive evolution of complex phenotypes.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
ABySS: A parallel assembler for short read sequence data
Jared T. Simpson,Kim Wong,Shaun D. Jackman,Jacqueline E. Schein,Steven J.M. Jones,Inanc Birol +5 more
TL;DR: ABySS (Assembly By Short Sequences), a parallelized sequence assembler, was developed and assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc, representing 68% of the reference human genome.
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