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Simon NM, Kim Y, Bautista DM, Dutton JR, Brem RB. Stem cell transcriptional profiles from mouse subspecies reveal cis -regulatory evolution at translation genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549406. [PMID: 37503246 PMCID: PMC10370129 DOI: 10.1101/2023.07.18.549406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis -regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.
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2
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Zintel TM, Pizzollo J, Claypool CG, Babbitt CC. Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees. Genome Biol Evol 2024; 16:evad239. [PMID: 38159045 PMCID: PMC10829071 DOI: 10.1093/gbe/evad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024] Open
Abstract
The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.
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Affiliation(s)
- Trisha M Zintel
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christopher G Claypool
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
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3
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Suresh H, Crow M, Jorstad N, Hodge R, Lein E, Dobin A, Bakken T, Gillis J. Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nat Ecol Evol 2023; 7:1930-1943. [PMID: 37667001 PMCID: PMC10627823 DOI: 10.1038/s41559-023-02186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic innovations remain poorly understood, in part because of the lack of high-quality cellular resolution data in human and non-human primates. Here, we take advantage of single-cell expression data from the middle temporal gyrus of five primates (human, chimp, gorilla, macaque and marmoset) to identify 57 homologous cell types and generate cell type-specific gene co-expression networks for comparative analysis. Although orthologue expression patterns are generally well conserved, we find 24% of genes with extensive differences between human and non-human primates (3,383 out of 14,131), which are also associated with multiple brain disorders. To assess the functional significance of gene expression differences in an evolutionary context, we evaluate changes in network connectivity across meta-analytic co-expression networks from 19 animals. We find that a subset of these genes has deeply conserved co-expression across all non-human animals, and strongly divergent co-expression relationships in humans (139 out of 3,383, <1% of primate orthologues). Genes with human-specific cellular expression and co-expression profiles (such as NHEJ1, GTF2H2, C2 and BBS5) typically evolve under relaxed selective constraints and may drive rapid evolutionary change in brain function.
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Affiliation(s)
- Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Alexander Dobin
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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4
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Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol 2023; 24:207. [PMID: 37697401 PMCID: PMC10496171 DOI: 10.1186/s13059-023-03019-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Affiliation(s)
- Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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5
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Colbran LL, Ramos-Almodovar FC, Mathieson I. A gene-level test for directional selection on gene expression. Genetics 2023; 224:iyad060. [PMID: 37036411 PMCID: PMC10213495 DOI: 10.1093/genetics/iyad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 04/11/2023] Open
Abstract
Most variants identified in human genome-wide association studies and scans for selection are noncoding. Interpretation of their effects and the way in which they contribute to phenotypic variation and adaptation in human populations is therefore limited by our understanding of gene regulation and the difficulty of confidently linking noncoding variants to genes. To overcome this, we developed a gene-wise test for population-specific selection based on combinations of regulatory variants. Specifically, we use the QX statistic to test for polygenic selection on cis-regulatory variants based on whether the variance across populations in the predicted expression of a particular gene is higher than expected under neutrality. We then applied this approach to human data, testing for selection on 17,388 protein-coding genes in 26 populations from the Thousand Genomes Project. We identified 45 genes with significant evidence (FDR<0.1) for selection, including FADS1, KHK, SULT1A2, ITGAM, and several genes in the HLA region. We further confirm that these signals correspond to plausible population-level differences in predicted expression. While the small number of significant genes (0.2%) is consistent with most cis-regulatory variation evolving under genetic drift or stabilizing selection, it remains possible that there are effects not captured in this study. Our gene-level QX score is independent of standard genomic tests for selection, and may therefore be useful in combination with traditional selection scans to specifically identify selection on regulatory variation. Overall, our results demonstrate the utility of combining population-level genomic data with functional data to understand the evolution of gene expression.
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Affiliation(s)
- Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Human and African ape myosin heavy chain content and the evolution of hominin skeletal muscle. Comp Biochem Physiol A Mol Integr Physiol 2023; 281:111415. [PMID: 36931425 DOI: 10.1016/j.cbpa.2023.111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8 Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals. The responsiveness of human skeletal muscle to behavioral interventions is also compared to the human-African ape differential. Humans are distinct from African apes and among a small group of terrestrial mammals whose pelvis and hind/lower limb muscle is slow fiber dominant, on average. Behavioral interventions, including immobilization, bed rest, spaceflight and exercise, can induce modest decreases and increases in human MyHC I content (i.e. -9.3% to 2.3%, n = 2033 subjects), but these shifts are much smaller than the mean human-African ape differential (i.e. 31%). Taken together, these results indicate muscle fiber content is likely an evolvable trait under selection in the hominin lineage. As such, we highlight potential targets of selection in the genome (e.g. regions that regulate MyHC content) that may play an important role in hominin skeletal muscle evolution.
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7
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Starr AL, Gokhman D, Fraser HB. Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits. Genome Biol 2023; 24:11. [PMID: 36658652 PMCID: PMC9850818 DOI: 10.1186/s13059-023-02846-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis-regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical organoids, we identify signatures of lineage-specific selection on genes related to saccharide metabolism, neurodegeneration, and primary cilia. We also highlight cis-regulatory divergence in CUX1 and EDNRB that may shape the trajectory of human brain development.
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Affiliation(s)
| | - David Gokhman
- Department of Biology, Stanford University, Stanford, CA, USA
- Present Address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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8
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Pal S, Oliver B, Przytycka TM. Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus. J Comput Biol 2023; 30:21-40. [PMID: 36037023 PMCID: PMC9917317 DOI: 10.1089/cmb.2022.0121] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gene expression evolution is typically modeled with the stochastic Ornstein-Uhlenbeck (OU) process. It has been suggested that the estimation of within-species variations using replicated data can increase the predictive power of such models, but this hypothesis has not been fully tested. We developed EvoGeneX, a computationally efficient implementation of the OU-based method that models within-species variation. Using extensive simulations, we show that modeling within-species variations and appropriate selection of species improve the performance of the model. Further, to facilitate a comparative analysis of expression evolution, we introduce a formal measure of evolutionary expression divergence for a group of genes using the rate and the asymptotic level of divergence. With these tools in hand, we performed the first-ever analysis of the evolution of gene expression across different body-parts, species, and sexes of the Drosophila genus. We observed that genes with adaptive expression evolution tend to be body-part specific, whereas the genes with constrained evolution tend to be shared across body-parts. Among the neutrally evolving gene expression patterns, gonads in both sexes have higher expression divergence relative to other tissues and the male gonads have even higher divergence than the female gonads. Among the evolutionarily constrained genes, the gonads show different divergence patterns, where the male gonads, and not the female gonads, show less constrained divergence than other body-parts. Finally, we show interesting examples of adaptive expression evolution, including adaptation of odor binding proteins.
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Affiliation(s)
- Soumitra Pal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA.,Address correspondence to: Dr. Brian Oliver, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.,Address correspondence to: Dr. Teresa M. Przytycka, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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9
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Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals (Basel) 2022; 12:ani12233432. [PMID: 36496954 PMCID: PMC9741297 DOI: 10.3390/ani12233432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
- Correspondence: (K.S.); (J.F.)
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.S.); (J.F.)
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10
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Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
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11
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Starr I, Seiffert-Sinha K, Sinha AA, Gokcumen O. Evolutionary context of psoriatic immune skin response. Evol Med Public Health 2022; 9:474-486. [PMID: 35154781 PMCID: PMC8830311 DOI: 10.1093/emph/eoab042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/22/2021] [Indexed: 12/18/2022] Open
Abstract
The skin is vital for protecting the body and perceiving external stimuli in the environment. Ability to adapt between environments is in part based on skin phenotypic plasticity, indicating evolved homeostasis between skin and environment. This homeostasis reflects the greater relationship between the body and the environment, and disruptions in this balance may lead to accumulation of susceptibility factors for autoimmune conditions like psoriasis. In this study, we examined the relationship between rapid, lineage-specific evolution of human skin and formation of psoriatic skin responses at the transcriptome level. We collected skin tissue biopsies from individuals with psoriasis and compared gene expression in psoriatic plaques to non-plaque psoriatic skin. We then compared these data with non-psoriatic skin transcriptome data from multiple primate species. We found 67 genes showing human-specific skin expression that are also differentially regulated in psoriatic skin; these genes are significantly enriched for skin barrier function, immunity and neuronal development. We identified six gene clusters with differential expression in the context of human evolution and psoriasis, suggesting underlying regulatory mechanisms in these loci. Human and psoriasis-specific enrichment of neuroimmune genes shows the importance of the ongoing evolved homeostatic relationship between skin and external environment. These results have implications for both evolutionary medicine and public health, using transcriptomic data to acknowledge the importance of an individual’s surroundings on their overall health. The skin is important for protecting the body from the environment and perceiving external stimuli, creating an evolved balance between skin and the environment. We compare skin gene expression in humans with psoriasis to humans and non-human primates without psoriasis to better understand human-specific evolutionary changes in the skin. Our results suggest important evolutionary links between skin perception, human-specific skin development and immune response.
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Affiliation(s)
- Izzy Starr
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Kristina Seiffert-Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Animesh A Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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12
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Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep 2021; 37:110057. [PMID: 34818542 PMCID: PMC8647622 DOI: 10.1016/j.celrep.2021.110057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology across species and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterize the transcriptional response of human colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We find that most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes. However, hundreds of host genes exhibit a divergent response, whereby they respond only to microbiomes from specific host species. Such genes are associated with intestinal diseases in humans, including inflammatory bowel disease and Crohn’s disease. Last, we find that inflammation-associated microbial species regulate the expression of host genes previously associated with inflammatory bowel disease, suggesting health-related consequences for species-specific host-microbiome interactions across hominids. Muehlbauer et al. investigate how variation between different hominid microbiomes drives host gene expression in colonic epithelial cell cultures. They find that host genes that respond only to microbiomes from a specific hominid species are linked to gastrointestinal diseases, suggesting implications for understanding how the microbiome can impact human health.
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Affiliation(s)
- Amanda L Muehlbauer
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Michael B Burns
- Department of Biology, Loyola University, Chicago, IL 60660, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NB, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NB, USA
| | - Klara Petrzelkova
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic; Liberec Zoo, Liberec, Czech Republic; The Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Camilla Cascardo
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Justyna Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA.
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13
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Huang YF. Dissecting genomic determinants of positive selection with an evolution-guided regression model. Mol Biol Evol 2021; 39:6379733. [PMID: 34597406 PMCID: PMC8763110 DOI: 10.1093/molbev/msab291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.
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Affiliation(s)
- Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
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14
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Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, Gauthier J. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus. J Evol Biol 2021; 34:1704-1721. [PMID: 34570954 DOI: 10.1111/jeb.13940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.
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Affiliation(s)
- Florence Piron-Prunier
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire Écologie, Évolution,Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | | | - Ammara Mohammad
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Corinne Blugeon
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jérémy Gauthier
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
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15
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Feng Y, Xu H, Liu J, Xie N, Gao L, He Y, Yao Y, Lv F, Zhang Y, Lu J, Zhang W, Li CY, Hu X, Yang Z, Xiao RP. Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates. Mol Biol Evol 2021; 38:2930-2945. [PMID: 33744959 PMCID: PMC8233513 DOI: 10.1093/molbev/msab083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cis-regulatory elements play important roles in tissue-specific gene expression and in the evolution of various phenotypes, and mutations in promoters and enhancers may be responsible for adaptations of species to environments. TRIM72 is a highly conserved protein that is involved in energy metabolism. Its expression in the heart varies considerably in primates, with high levels of expression in Old World monkeys and near absence in hominids. Here, we combine phylogenetic hypothesis testing and experimentation to demonstrate that mutations in promoter are responsible for the differences among primate species in the heart-specific expression of TRIM72. Maximum likelihood estimates of lineage-specific substitution rates under local-clock models show that relative to the evolutionary rate of introns, the rate of promoter was accelerated by 78% in the common ancestor of Old World monkeys, suggesting a role for positive selection in the evolution of the TRIM72 promoter, possibly driven by selective pressure due to changes in cardiac physiology after species divergence. We demonstrate that mutations in the TRIM72 promoter account for the differential myocardial TRIM72 expression of the human and the rhesus macaque. Furthermore, changes in TRIM72 expression alter the expression of genes involved in oxidative phosphorylation, which in turn affects mitochondrial respiration and cardiac energy capacity. On a broader timescale, phylogenetic regression analyses of data from 29 mammalian species show that mammals with high cardiac expression of TRIM72 have high heart rate, suggesting that the expression changes of TRIM72 may be related to differences in the heart physiology of those species.
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Affiliation(s)
- Yuanqing Feng
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Hongzhan Xu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jinghao Liu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ning Xie
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lei Gao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanyun He
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yuan Yao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fengxiang Lv
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yan Zhang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian Lu
- Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Gene Research, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Wei Zhang
- Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Gene Research, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Chuan-Yun Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinli Hu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Rui-Ping Xiao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Biomembrane and Membrane Biotechnology, Beijing, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
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16
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Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. eLife 2020; 9:59929. [PMID: 33084571 PMCID: PMC7644215 DOI: 10.7554/elife.59929] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.
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Affiliation(s)
| | - Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, United States
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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17
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Luo Z, Xiong J, Xia H, Ma X, Gao M, Wang L, Liu G, Yu X, Luo L. Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought-prone agroecosystem. Evol Appl 2020; 13:2484-2496. [PMID: 33005236 PMCID: PMC7513727 DOI: 10.1111/eva.13054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Transcriptomic divergence drives plant ecological adaptation. Upland rice is differentiated in drought tolerance from lowland rice during its adaptation to the drought-prone environment. They provide a good system to learn the evolution of drought tolerance in rice. METHODS AND RESULTS We estimate morphological differences between the two rice ecotypes under well-watered and drought conditions, as well as their genetic and transcriptomic divergences by the high-throughput sequencing. Upland rice possesses higher expression diversity than lowland rice does. Thousands of genes exhibit expression divergences between the two rice ecotypes, which contributes to their morphological differences in drought tolerance. These transcriptomic divergences contribute to drought adaptation of upland rice during its domestication. Mutations in transcriptional regulatory regions, which cause presence and absence of cis-elements, are the cause of expression divergence. About 15.3% transcriptionally selected genes also receive sequence-based selection in upland or lowland ecotype. Some highly differentiated genes promote the transcriptomic divergence between rice ecotypes via gene co-expression network. In addition, we also detected transcriptomic trade-offs between drought tolerance and productivity. DISCUSSION Many key genes, which promote transcriptomic adaptation to drought in upland rice, have great prospective in breeding water-saving and drought-resistant rice. Meanwhile, appropriate strategies are required in breeding to overcome the potential transcriptomic trade-off.
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Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Jie Xiong
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Hui Xia
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center Shanghai China
| | - Min Gao
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Lei Wang
- Shanghai Agrobiological Gene Center Shanghai China
| | - Guolan Liu
- Shanghai Agrobiological Gene Center Shanghai China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center Shanghai China
| | - Lijun Luo
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
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18
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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19
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Miao B, Fu S, Lyu C, Gontarz P, Wang T, Zhang B. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biol 2020; 21:255. [PMID: 32988383 PMCID: PMC7520981 DOI: 10.1186/s13059-020-02164-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology. RESULTS We examine the epigenetic dynamics of mouse TEs during the development of five tissues: intestine, liver, lung, stomach, and kidney. We found that TEs are associated with over 20% of open chromatin regions during development. Close to half of these accessible TEs are only activated in a single tissue and a specific developmental stage. Most accessible TEs are rodent-specific. Across these five tissues, 453 accessible TEs are found to create the transcription start sites of downstream genes in mouse, including 117 protein-coding genes and 144 lincRNA genes, 93.7% of which are mouse-specific. Species-specific TE-derived transcription start sites are found to drive the expression of tissue-specific genes and change their tissue-specific expression patterns during evolution. CONCLUSION Our results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Shuhua Fu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Cheng Lyu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Paul Gontarz
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA.
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20
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Anderson JA, Vilgalys TP, Tung J. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Curr Opin Genet Dev 2020; 62:16-22. [PMID: 32569794 PMCID: PMC7483836 DOI: 10.1016/j.gde.2020.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
Comparative analyses have played a key role in understanding how gene regulatory evolution contributes to primate phenotypic diversity. Recently, these studies have expanded to include a wider range of species, within-population as well as interspecific analyses, and research on wild as well as captive individuals. This expansion provides context for understanding genetic and environmental effects on gene regulation in humans, including the importance of the pathogen and social environments. Although taxonomic representation remains biased, inclusion of more species has also begun to reveal the evolutionary processes that explain whether and when gene regulation is conserved. Together, this work highlights how studies in other primates contribute to understanding evolution in our own lineage, and we conclude by identifying promising avenues for future work.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya; Duke Population Research Institute, Duke University, Durham, NC 27708, USA.
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21
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Bauernfeind AL, Babbitt CC. Metabolic changes in human brain evolution. Evol Anthropol 2020; 29:201-211. [PMID: 32329960 DOI: 10.1002/evan.21831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022]
Abstract
Because the human brain is considerably larger than those of other primates, it is not surprising that its energy requirements would far exceed that of any of the species within the order. Recently, the development of stem cell technologies and single-cell transcriptomics provides novel ways to address the question of what specific genomic changes underlie the human brain's unique phenotype. In this review, we consider what is currently known about human brain metabolism using a variety of methods from brain imaging and stereology to transcriptomics. Next, we examine novel opportunities that stem cell technologies and single-cell transcriptomics provide to further our knowledge of human brain energetics. These new experimental approaches provide the ability to elucidate the functional effects of changes in genetic sequence and expression levels that potentially had a profound impact on the evolution of the human brain.
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Affiliation(s)
- Amy L Bauernfeind
- Department of Neuroscience, Washington University Medical School, St. Louis, Missouri, USA.,Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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22
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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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23
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Housman G, Quillen EE, Stone AC. Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:34-49. [PMID: 32170728 DOI: 10.1002/ajpa.24041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. MATERIALS AND METHODS First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). RESULTS Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. DISCUSSION Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
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24
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Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol 2020; 20:33. [PMID: 32106815 PMCID: PMC7045612 DOI: 10.1186/s12862-020-1595-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/11/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression. RESULTS We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential. CONCLUSIONS The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
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25
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Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res 2020; 30:250-262. [PMID: 31953346 PMCID: PMC7050529 DOI: 10.1101/gr.254904.119] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/02/2020] [Indexed: 01/02/2023]
Abstract
Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein–protein interaction networks.
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Affiliation(s)
- Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Julien Roux
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4031 Basel, Switzerland
| | | | - Nicholas E Banovich
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Raquel Garcia Perez
- Universitat Pompeu Fabra, Institute of Evolutionary Biology, 88 08003 Barcelona, Spain
| | - Chiaowen Joyce Hsiao
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Ittai Eres
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Tomas Marques-Bonet
- Universitat Pompeu Fabra, Institute of Evolutionary Biology, 88 08003 Barcelona, Spain.,Passeig de Lluís Companys, Catalan Institution of Research and Advanced Studies, 23 08010 Barcelona, Spain.,Barcelona Institute of Science and Technology, Centre for Genomic Regulation, 88 08003 Barcelona, Spain.,Universitat Autònoma de Barcelona, Institut Català de Paleontologia Miquel Crusafont, 08193 Barcelona, Spain
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.,Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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26
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Zheng XM, Chen J, Pang HB, Liu S, Gao Q, Wang JR, Qiao WH, Wang H, Liu J, Olsen KM, Yang QW. Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication. SCIENCE ADVANCES 2019; 5:eaax3619. [PMID: 32064312 PMCID: PMC6989341 DOI: 10.1126/sciadv.aax3619] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/30/2019] [Indexed: 05/17/2023]
Abstract
Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.
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Affiliation(s)
- X. M. Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - H. B. Pang
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - S. Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Q. Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. R. Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - W. H. Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - H. Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
| | - K. M. Olsen
- Biology Department, Campus Box 1137, Washington University, St. Louis, MO 63130, USA
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
| | - Q. W. Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
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27
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Böck J, Remmele CW, Dittrich M, Müller T, Kondova I, Persengiev S, Bontrop RE, Ade CP, Kraus TFJ, Giese A, El Hajj N, Schneider E, Haaf T. Cell Type and Species-specific Patterns in Neuronal and Non-neuronal Methylomes of Human and Chimpanzee Cortices. Cereb Cortex 2019; 28:3724-3739. [PMID: 30085031 PMCID: PMC6132288 DOI: 10.1093/cercor/bhy180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/13/2018] [Indexed: 12/04/2022] Open
Abstract
Epigenetic changes have likely contributed to the large size and enhanced cognitive abilities of the human brain which evolved within the last 2 million years after the human–chimpanzee split. Using reduced representation bisulfite sequencing, we have compared the methylomes of neuronal and non-neuronal cells from 3 human and 3 chimpanzee cortices. Differentially methylated regions (DMRs) with genome-wide significance were enriched in specific genomic regions. Intraspecific methylation differences between neuronal and non-neuronal cells were approximately 3 times more abundant than interspecific methylation differences between human and chimpanzee cell types. The vast majority (>90%) of human intraspecific DMRs (including DMRs in retrotransposons) were hypomethylated in neurons, compared with glia. Intraspecific DMRs were enriched in genes associated with different neuropsychiatric disorders. Interspecific DMRs were enriched in genes showing human-specific brain histone modifications. Human–chimpanzee methylation differences were much more frequent in non-neuronal cells (n. DMRs = 666) than in neurons (n. DMRs = 96). More than 95% of interspecific DMRs in glia were hypermethylated in humans. Although without an outgroup we cannot assign whether a change in methylation occurred in the human or chimpanzee lineage, our results are consistent with a wave of methylation affecting several hundred non-neuronal genes during human brain evolution.
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Affiliation(s)
- Julia Böck
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Christian W Remmele
- Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center, 2288 GJ Rijswijk, The Netherlands
| | | | - Ronald E Bontrop
- Biomedical Primate Research Center, 2288 GJ Rijswijk, The Netherlands
| | - Carsten P Ade
- Institute of Biochemistry and Molecular Biology, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research, Ludwig Maximilians University Munich, Munich, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig Maximilians University Munich, Munich, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Eberhard Schneider
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
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28
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Edsall LE, Berrio A, Majoros WH, Swain-Lenz D, Morrow S, Shibata Y, Safi A, Wray GA, Crawford GE, Allen AS. Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. Genome Biol Evol 2019; 11:3035-3053. [PMID: 31599933 PMCID: PMC6821351 DOI: 10.1093/gbe/evz218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address this important gap in knowledge, we developed a new method to identify DNase I Hypersensitive (DHS) sites with differential chromatin accessibility between species using a joint modeling approach. Our method overcomes several limitations inherent to conventional threshold-based pairwise comparisons that become increasingly apparent as the number of species analyzed rises. Our approach employs a single quantitative test which is more sensitive than existing pairwise methods. To illustrate, we applied our joint approach to DHS sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and rhesus macaque). We identified 89,744 DHS sites, of which 41% are identified as differential between species using the joint model compared with 33% using the conventional pairwise approach. The joint model provides a principled approach to distinguishing single from multiple chromatin accessibility changes among species. We found that nondifferential DHS sites are enriched for nucleotide conservation. Differential DHS sites with decreased chromatin accessibility relative to rhesus macaque occur more commonly near transcription start sites (TSS), while those with increased chromatin accessibility occur more commonly distal to TSS. Further, differential DHS sites near TSS are less cell type-specific than more distal regulatory elements. Taken together, these results point to distinct classes of DHS sites, each with distinct characteristics of selection, genomic location, and cell type specificity.
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Affiliation(s)
- Lee E Edsall
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
- University Program in Genetics and Genomics, Duke University
| | | | | | | | | | - Yoichiro Shibata
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University
- Department of Biology, Duke University
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University
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29
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Suner A. Clustering methods for single-cell RNA-sequencing expression data: performance evaluation with varying sample sizes and cell compositions. Stat Appl Genet Mol Biol 2019; 18:/j/sagmb.2019.18.issue-5/sagmb-2019-0004/sagmb-2019-0004.xml. [PMID: 31646845 DOI: 10.1515/sagmb-2019-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A number of specialized clustering methods have been developed so far for the accurate analysis of single-cell RNA-sequencing (scRNA-seq) expression data, and several reports have been published documenting the performance measures of these clustering methods under different conditions. However, to date, there are no available studies regarding the systematic evaluation of the performance measures of the clustering methods taking into consideration the sample size and cell composition of a given scRNA-seq dataset. Herein, a comprehensive performance evaluation study of 11 selected scRNA-seq clustering methods was performed using synthetic datasets with known sample sizes and number of subpopulations, as well as varying levels of transcriptome complexity. The results indicate that the overall performance of the clustering methods under study are highly dependent on the sample size and complexity of the scRNA-seq dataset. In most of the cases, better clustering performances were obtained as the number of cells in a given expression dataset was increased. The findings of this study also highlight the importance of sample size for the successful detection of rare cell subpopulations with an appropriate clustering tool.
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Affiliation(s)
- Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Bornova, İzmir, Turkey
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30
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Eres IE, Luo K, Hsiao CJ, Blake LE, Gilad Y. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. PLoS Genet 2019; 15:e1008278. [PMID: 31323043 PMCID: PMC6668850 DOI: 10.1371/journal.pgen.1008278] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 07/31/2019] [Accepted: 06/28/2019] [Indexed: 12/22/2022] Open
Abstract
A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-seq to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as topologically associating domains (TADs), are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human stem cells. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrate that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution. The way in which a genome folds affects the regulation of gene expression. This is often due to loops in the three-dimensional structure that bring linearly distant genes and regulatory elements into close proximity. Most studies examining three-dimensional structure genome-wide are limited to a single species. In this study, we compared three-dimensional structure in the genomes of induced pluripotent stem cells from humans and chimpanzees. We collected gene expression data from the same samples, which allowed us to assess the contribution of three-dimensional chromatin conformation to gene regulatory evolution in primates. Our results demonstrate that gene expression differences between the species may often be mediated by differences in three-dimensional genomic interactions. Our data also suggest that large-scale chromatin structures (i.e. topologically associating domains, TADs) are not well conserved in their placement across species. We hope the analytical paradigms we present here could serve as a basis for future comparative studies of three-dimensional genome organization, elucidating the putative functional regulatory loci driving speciation.
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Affiliation(s)
- Ittai E. Eres
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Chiaowen Joyce Hsiao
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Lauren E. Blake
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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31
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Vilgalys TP, Rogers J, Jolly CJ, Baboon Genome Analysis, Mukherjee S, Tung J. Evolution of DNA Methylation in Papio Baboons. Mol Biol Evol 2019; 36:527-540. [PMID: 30521003 PMCID: PMC6389319 DOI: 10.1093/molbev/msy227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels in blood samples from five of the six extant species of the baboon genus Papio (4-14 individuals per species). This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper timescales (0.380-1.4 My). In contrast to studies in human populations, but similar to studies in great apes, DNA methylation profiles clearly mirror genetic and geographic structure. Divergence in DNA methylation proceeds fastest in unannotated regions of the genome and slowest in regions of the genome that are likely more constrained at the sequence level (e.g., gene exons). Both heuristic approaches and Ornstein-Uhlenbeck models suggest that DNA methylation levels at a small set of sites have been affected by positive selection, and that this class is enriched in functionally relevant contexts, including promoters, enhancers, and CpG islands. Our results thus indicate that the rate and distribution of DNA methylation changes across the genome largely mirror genetic structure. However, at some CpG sites, DNA methylation levels themselves may have been a target of positive selection, pointing to loci that could be important in connecting sequence variation to fitness-related traits.
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Affiliation(s)
- Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY
- Center for the Study of Human Origins, New York University, New York, NY
- New York Consortium for Evolutionary Primatology, New York, NY
| | | | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC
- Department of Mathematics, Duke University, Durham, NC
- Department of Computer Science, Duke University, Durham, NC
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC
- Department of Biology, Duke University, Durham, NC
- Duke University Population Research Institute, Duke University, Durham, NC
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
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32
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Parker DJ, Bast J, Jalvingh K, Dumas Z, Robinson-Rechavi M, Schwander T. Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes. Mol Biol Evol 2019; 36:350-364. [PMID: 30445505 PMCID: PMC6404633 DOI: 10.1093/molbev/msy217] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Asexual reproduction has evolved repeatedly from sexual ancestors across a wide range of taxa. Whereas the costs and benefits associated with asexuality have received considerable attention, the molecular changes underpinning the evolution of asexual reproduction remain relatively unexplored. In particular, it is completely unknown whether the repeated evolution of asexual phenotypes involves similar molecular changes, as previous studies have focused on changes occurring in single lineages. Here, we investigate the extent of convergent gene expression changes across five independent transitions to asexuality in stick insects. We compared gene expression of asexual females to females of close sexual relatives in whole-bodies, reproductive tracts, and legs. We identified a striking amount of convergent gene expression change (up to 8% of genes), greatly exceeding that expected by chance. Convergent changes were also tissue-specific, and most likely driven by selection for functional changes. Genes showing convergent changes in the reproductive tract were associated with meiotic spindle formation and centrosome organization. These genes are particularly interesting as they can influence the production of unreduced eggs, a key barrier to asexual reproduction. Changes in legs and whole-bodies were likely involved in female sexual trait decay, with enrichment in terms such as sperm-storage and pigmentation. By identifying changes occurring across multiple independent transitions to asexuality, our results provide a rare insight into the molecular basis of asexual phenotypes and suggest that the evolutionary path to asexuality is highly constrained, requiring repeated changes to the same key genes.
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Affiliation(s)
- Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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33
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Izquierdo A, Fahrenberger M, Persampieri T, Benedict MQ, Giles T, Catteruccia F, Emes RD, Dottorini T. Evolution of gene expression levels in the male reproductive organs of Anopheles mosquitoes. Life Sci Alliance 2019; 2:e201800191. [PMID: 30623175 PMCID: PMC6315087 DOI: 10.26508/lsa.201800191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Modifications in gene expression determine many of the phenotypic differentiations between closely related species. This is particularly evident in reproductive tissues, where evolution of genes is more rapid, facilitating the appearance of distinct reproductive characteristics which may lead to species isolation and phenotypic variation. Large-scale, comparative analyses of transcript expression levels have been limited until recently by lack of inter-species data mining solutions. Here, by combining expression normalisation across lineages, multivariate statistical analysis, evolutionary rate, and protein-protein interaction analysis, we investigate ortholog transcripts in the male accessory glands and testes across five closely related species in the Anopheles gambiae complex. We first demonstrate that the differentiation by transcript expression is consistent with the known Anopheles phylogeny. Then, through clustering, we discover groups of transcripts with tissue-dependent expression patterns conserved across lineages, or lineage-dependent patterns conserved across tissues. The strongest associations with reproductive function, transcriptional regulatory networks, protein-protein subnetworks, and evolutionary rate are found for the groups of transcripts featuring large expression differences in lineage or tissue-conserved patterns.
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Affiliation(s)
- Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Martin Fahrenberger
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Persampieri
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Mark Q Benedict
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Tom Giles
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Richard D Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK.,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
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34
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Assis R. Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. Genome Biol Evol 2019; 11:207-219. [PMID: 30398650 PMCID: PMC6331041 DOI: 10.1093/gbe/evy245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 02/02/2023] Open
Abstract
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.
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Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park
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35
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Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, Palma FD, Regev A. A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Res 2018; 29:53-63. [PMID: 30552105 PMCID: PMC6314168 DOI: 10.1101/gr.237636.118] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/27/2018] [Indexed: 01/09/2023]
Abstract
The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene's expression, parameterize the distribution of each gene's optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.
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Affiliation(s)
- Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Division of Health Science and Technology, MIT, Cambridge, Massachusetts 02139, USA
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Beryl B Cummings
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Noga Rogel
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | | | - Federica di Palma
- Earlham Institute, Norwich NR4 7UZ, United Kingdom.,Department of Biological and Medical Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology and Koch Institute, MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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36
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Sevane N, Martínez R, Bruford MW. Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors. Anim Genet 2018; 50:15-26. [DOI: 10.1111/age.12731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- N. Sevane
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
| | - R. Martínez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica); Centro de Investigaciones Tibaitatá; km 14 via Bogotá 250047 Mosquera Colombia
| | - M. W. Bruford
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
- Sustainable Places Research Institute; Cardiff University; Cardiff CF10 3BA UK
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37
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Wang SH, Hsiao CJ, Khan Z, Pritchard JK. Post-translational buffering leads to convergent protein expression levels between primates. Genome Biol 2018; 19:83. [PMID: 29950183 PMCID: PMC6020354 DOI: 10.1186/s13059-018-1451-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/10/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription. RESULTS To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee, and rhesus macaque. We further integrated messenger RNA and protein level measurements collected from matching cell lines. We find that, in addition to transcriptional regulation, the major factor determining protein level divergence between human and closely related species is post-translational buffering. Inter-species divergence in transcription is generally propagated to the level of protein translation. In contrast, gene expression divergence is often attenuated post-translationally, potentially mediated through post-translational modifications. CONCLUSIONS Results from our analysis indicate that post-translational buffering is a conserved mechanism that led to relaxation of selective constraint on transcript levels in humans.
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Affiliation(s)
- Sidney H. Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX USA
| | | | - Zia Khan
- Genentech, 1 DNA Way, South San Francisco, CA USA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA USA
- Department of Biology, Stanford University, Stanford, CA USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA USA
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38
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Xu C, Li Q, Efimova O, He L, Tatsumoto S, Stepanova V, Oishi T, Udono T, Yamaguchi K, Shigenobu S, Kakita A, Nawa H, Khaitovich P, Go Y. Human-specific features of spatial gene expression and regulation in eight brain regions. Genome Res 2018; 28:1097-1110. [PMID: 29898898 PMCID: PMC6071643 DOI: 10.1101/gr.231357.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/04/2018] [Indexed: 01/22/2023]
Abstract
Molecular maps of the human brain alone do not inform us of the features unique to humans. Yet, the identification of these features is important for understanding both the evolution and nature of human cognition. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, a gibbon, and macaques. An analysis of spatial transcriptome trajectories across eight brain regions in four primate species revealed 1851 genes showing human-specific transcriptome differences in one or multiple brain regions, in contrast to 240 chimpanzee-specific differences. More than half of these human-specific differences represented elevated expression of genes enriched in neuronal and astrocytic markers in the human hippocampus, whereas the rest were enriched in microglial markers and displayed human-specific expression in several frontal cortical regions and the cerebellum. An analysis of the predicted regulatory interactions driving these differences revealed the role of transcription factors in species-specific transcriptome changes, and epigenetic modifications were linked to spatial expression differences conserved across species.
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Affiliation(s)
- Chuan Xu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Liu He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 4448585, Japan
| | - Vita Stepanova
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Takao Oishi
- Primate Research Institute, Kyoto University, Inuyama, Aichi 4848506, Japan
| | - Toshifumi Udono
- Kumamoto Sanctuary, Wildlife Research Center, Kyoto University, Uki, Kumamoto 8693201, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi 4448585, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi 4448585, Japan.,School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 4448585, Japan
| | - Akiyoshi Kakita
- Brain Research Institute, Niigata University, Niigata 9518585, Japan
| | - Hiroyuki Nawa
- Brain Research Institute, Niigata University, Niigata 9518585, Japan
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow 143026, Russia.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,Comparative Biology Laboratory, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 4448585, Japan.,School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 4448585, Japan.,Department of Physiological Sciences, National Institute for Physiological Sciences, Okazaki, Aichi 4448585, Japan
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39
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Tine M. Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations. Int J Genomics 2017; 2017:1258396. [PMID: 29201893 PMCID: PMC5672613 DOI: 10.1155/2017/1258396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/24/2017] [Accepted: 09/18/2017] [Indexed: 11/17/2022] Open
Abstract
The present work examines the induction of the band 3 anion transport protein, mitogen-activated protein kinase, and lactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.
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Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (UFR S2ATA), Universite Gaston Berger (UGB), Route de Ngallele BP 234, Saint-Louis, Senegal
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40
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Lin HY, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS. Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS. Genome Biol 2017; 18:192. [PMID: 29041960 PMCID: PMC5645915 DOI: 10.1186/s13059-017-1328-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a Bayesian-based method for genome-wide association studies (GWAS) in which RNA-seq-based measures of transcript accumulation are used as explanatory variables (eRD-GWAS). The ability of eRD-GWAS to identify true associations between gene expression variation and phenotypic diversity is supported by analyses of RNA co-expression networks, protein-protein interaction networks, and gene regulatory networks. Genes associated with 13 traits were identified using eRD-GWAS on a panel of 369 maize inbred lines. Predicted functions of many of the resulting trait-associated genes are consistent with the analyzed traits. Importantly, transcription factors are significantly enriched among trait-associated genes identified with eRD-GWAS. CONCLUSIONS eRD-GWAS is a powerful tool for associating genes with traits and is complementary to SNP-based GWAS. Our eRD-GWAS results are consistent with the hypothesis that genetic variation in transcription factor expression contributes substantially to phenotypic diversity.
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Affiliation(s)
- Hung-Ying Lin
- Department of Agronomy, Iowa State University, 2035 B Roy J Carver Co-Lab, Ames, IA, 50011-3650, USA.,Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA
| | - Qiang Liu
- Department of Agronomy, Iowa State University, 2035 B Roy J Carver Co-Lab, Ames, IA, 50011-3650, USA.,Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA
| | - Xiao Li
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA.,Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA, 50011-3650, USA.,The Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142-1403, USA
| | - Jinliang Yang
- Department of Agronomy, Iowa State University, 2035 B Roy J Carver Co-Lab, Ames, IA, 50011-3650, USA.,Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616-5270, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, 68583-0660, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, 2035 B Roy J Carver Co-Lab, Ames, IA, 50011-3650, USA.,Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA.,Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Yinlian Huang
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing, 100193, China.,DATA Biotechnology Beijing Co. Ltd, Beijing, 102206, China
| | - Michael J Scanlon
- Plant Biology Section, Cornell University, Ithaca, New York, 14850, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, 50011-1210, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, 2035 B Roy J Carver Co-Lab, Ames, IA, 50011-3650, USA. .,Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, 50011-3650, USA. .,Department of Genetics, Developmental and Cellular Biology, Iowa State University, Ames, IA, 50011-3650, USA. .,Department of Plant Genetics & Breeding, China Agricultural University, Beijing, 100193, China.
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41
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Nourmohammad A, Rambeau J, Held T, Kovacova V, Berg J, Lässig M. Adaptive Evolution of Gene Expression in Drosophila. Cell Rep 2017; 20:1385-1395. [DOI: 10.1016/j.celrep.2017.07.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 04/15/2017] [Accepted: 07/13/2017] [Indexed: 01/17/2023] Open
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42
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Dasmeh P, Kepp KP. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes. Cell Mol Life Sci 2017; 74:3023-3037. [PMID: 28389720 PMCID: PMC11107616 DOI: 10.1007/s00018-017-2519-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
Abstract
Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million years, significantly higher than in other primates and rodents, although these paradoxically generally evolve much faster. The high evolutionary rate was partly due to relaxation of some selection pressures and partly to distinct positive selection of SOD1 in great apes. We then show that higher stability and net charge and changes at the dimer interface were selectively introduced upon separation from old world monkeys and lesser apes (gibbons). Consequently, human, chimpanzee and gorilla SOD1s have a net charge of -6 at physiological pH, whereas the closely related gibbons and macaques have -3. These features consistently point towards selection against the malicious aggregation effects of elevated SOD1 levels in long-living great apes. The findings mirror the impact of human SOD1 mutations that reduce net charge and/or stability and cause ALS, a motor neuron disease characterized by oxidative stress and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging.
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Affiliation(s)
- Pouria Dasmeh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Biochemistry and Cedergren Center for Bioinformatics and Genomics, Faculty of Medicine, University of Montreal, 2900 Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, 2800, Kongens Lyngby, Denmark.
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43
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Babbitt CC, Haygood R, Nielsen WJ, Wray GA. Gene expression and adaptive noncoding changes during human evolution. BMC Genomics 2017; 18:435. [PMID: 28583075 PMCID: PMC5460488 DOI: 10.1186/s12864-017-3831-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/31/2017] [Indexed: 01/14/2023] Open
Abstract
Background Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Results Here we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations. Conclusions Consistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3831-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Courtney C Babbitt
- Department of Biology, Duke University, Durham, NC, 27708, USA. .,Institute for Genome Sciences & Policy, Duke University, Durham, NC, 27708, USA. .,Present Address: Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| | | | | | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, 27708, USA.,Institute for Genome Sciences & Policy, Duke University, Durham, NC, 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
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44
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Smith G, Macias-Muñoz A, Briscoe AD. Gene Duplication and Gene Expression Changes Play a Role in the Evolution of Candidate Pollen Feeding Genes in Heliconius Butterflies. Genome Biol Evol 2016; 8:2581-96. [PMID: 27553646 PMCID: PMC5010911 DOI: 10.1093/gbe/evw180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Heliconius possess a unique ability among butterflies to feed on pollen. Pollen feeding significantly extends their lifespan, and is thought to have been important to the diversification of the genus. We used RNA sequencing to examine feeding-related gene expression in the mouthparts of four species of Heliconius and one nonpollen feeding species, Eueides isabella. We hypothesized that genes involved in morphology and protein metabolism might be upregulated in Heliconius because they have longer proboscides than Eueides, and because pollen contains more protein than nectar. Using de novo transcriptome assemblies, we tested these hypotheses by comparing gene expression in mouthparts against antennae and legs. We first looked for genes upregulated in mouthparts across all five species and discovered several hundred genes, many of which had functional annotations involving metabolism of proteins (cocoonase), lipids, and carbohydrates. We then looked specifically within Heliconius where we found eleven common upregulated genes with roles in morphology (CPR cuticle proteins), behavior (takeout-like), and metabolism (luciferase-like). Closer examination of these candidates revealed that cocoonase underwent several duplications along the lineage leading to heliconiine butterflies, including two Heliconius-specific duplications. Luciferase-like genes also underwent duplication within lepidopterans, and upregulation in Heliconius mouthparts. Reverse-transcription PCR confirmed that three cocoonases, a peptidase, and one luciferase-like gene are expressed in the proboscis with little to no expression in labial palps and salivary glands. Our results suggest pollen feeding, like other dietary specializations, was likely facilitated by adaptive expansions of preexisting genes—and that the butterfly proboscis is involved in digestive enzyme production.
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Affiliation(s)
- Gilbert Smith
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
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45
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Saber MM, Adeyemi Babarinde I, Hettiarachchi N, Saitou N. Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. Genome Biol Evol 2016; 8:2076-92. [PMID: 27289096 PMCID: PMC4987104 DOI: 10.1093/gbe/evw132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.
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Affiliation(s)
- Morteza Mahmoudi Saber
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Isaac Adeyemi Babarinde
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Nilmini Hettiarachchi
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Naruya Saitou
- Department of Biological Sciences, Graduate School of Science, University of Tokyo Division of Population Genetics, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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46
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Bailey J. Monkey-based research on human disease: the implications of genetic differences. Altern Lab Anim 2016; 42:287-317. [PMID: 25413291 DOI: 10.1177/026119291404200504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assertions that the use of monkeys to investigate human diseases is valid scientifically are frequently based on a reported 90-93% genetic similarity between the species. Critical analyses of the relevance of monkey studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for monkeys to constitute good models for research, and that monkey data do not translate well to progress in clinical practice for humans. Salient examples include the failure of new drugs in clinical trials, the highly different infectivity and pathology of SIV/HIV, and poor extrapolation of research on Alzheimer's disease, Parkinson's disease and stroke. The major molecular differences underlying these inter-species phenotypic disparities have been revealed by comparative genomics and molecular biology - there are key differences in all aspects of gene expression and protein function, from chromosome and chromatin structure to post-translational modification. The collective effects of these differences are striking, extensive and widespread, and they show that the superficial similarity between human and monkey genetic sequences is of little benefit for biomedical research. The extrapolation of biomedical data from monkeys to humans is therefore highly unreliable, and the use of monkeys must be considered of questionable value, particularly given the breadth and potential of alternative methods of enquiry that are currently available to scientists.
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Affiliation(s)
- Jarrod Bailey
- New England Anti-Vivisection Society (NEAVS), Boston, MA, USA
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47
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Abstract
As a species, we possess unique biological features that distinguish us from other primates. Here, we review recent efforts to identify changes in gene regulation that drove the evolution of novel human phenotypes. We discuss genotype-directed comparisons of human and nonhuman primate genomes to identify human-specific genetic changes that may encode new regulatory functions. We also review phenotype-directed approaches, which use comparisons of gene expression or regulatory function in homologous human and nonhuman primate cells and tissues to identify changes in expression levels or regulatory activity that may be due to genetic changes in humans. Together, these studies are beginning to reveal the landscape of regulatory innovation in human evolution and point to specific regulatory changes for further study. Finally, we highlight two novel strategies to model human-specific regulatory functions in vivo: primate induced pluripotent stem cells and the generation of humanized mice by genome editing.
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Affiliation(s)
- Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510;
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510; .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510
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48
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Advani AS, Chen AY, Babbitt CC. Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee. EVOLUTION MEDICINE AND PUBLIC HEALTH 2016; 2016:110-6. [PMID: 26971204 PMCID: PMC4804348 DOI: 10.1093/emph/eow010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/17/2016] [Indexed: 12/17/2022]
Abstract
It has been documented that there are differences in disease susceptibilities between humans and non-human primates. We investigate one of these differences in fibroblasts to examine differences in cellular adhesion between humans and chimpanzees using microscopy and gene expression and have found significant differences in both datasets. These results suggest that human and chimpanzee fibroblasts may have somewhat different adhesive properties, which could play a role in differential disease phenotypes and responses to external factors. There are a number of documented differences between humans and our closest relatives in responses to wound healing and in disease susceptibilities, suggesting a differential cellular response to certain environmental factors. In this study, we sought to look at a specific cell type, fibroblasts, to examine differences in cellular adhesion between humans and chimpanzees in visualized cells and in gene expression. We have found significant differences in the number of focal adhesions between primary human and chimpanzee fibroblasts. Additionally, we see that adhesion related gene ontology categories are some of the most differentially expressed between human and chimpanzee in normal fibroblast cells. These results suggest that human and chimpanzee fibroblasts may have somewhat different adhesive properties, which could play a role in differential disease phenotypes and responses to external factors.
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Affiliation(s)
| | - Annie Y Chen
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Courtney C Babbitt
- Department of Biology, Duke University, Durham, NC 27708, USA Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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49
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Abstract
A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.
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Guo J, Liu R, Huang L, Zheng XM, Liu PL, Du YS, Cai Z, Zhou L, Wei XH, Zhang FM, Ge S. Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species. Mol Biol Evol 2015; 33:62-78. [PMID: 26362653 DOI: 10.1093/molbev/msv196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5' flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.
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Affiliation(s)
- Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ping-Li Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Hua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China
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