1
|
Calamari ZT, Song A, Cohen E, Akter M, Roy RD, Hallikas O, Christensen MM, Li P, Marangoni P, Jernvall J, Klein OD. Vole genomics links determinate and indeterminate growth of teeth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572015. [PMID: 38187646 PMCID: PMC10769287 DOI: 10.1101/2023.12.18.572015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells responsible for tooth crown growth are lost at the onset of tooth root formation. Genetic signaling that initiates this loss is difficult to study with the ever-growing incisor and rooted molars of mice, the most common mammalian dental model species, because signals for root formation overlap with signals that pattern tooth size and shape (i.e., cusp patterns). Different species of voles (Cricetidae, Rodentia, Glires) have evolved rooted and unrooted molars that have similar size and shape, providing alternative models for studying roots. We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. We identified 15 dental genes with changing synteny relationships and six dental genes undergoing positive selection across Glires, two of which were undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Decreased expression of both genes in prairie voles with unrooted molars compared to bank voles supports the presence of positive selection and may underlie differences in root formation. Bulk transcriptomics analyses of embryonic molar development in bank voles also demonstrated conserved patterns of dental gene expression compared to mice, with species-specific variation likely related to developmental timing and morphological differences between mouse and vole molars. Our results support ongoing evolution of dental genes across Glires, revealing the complex evolutionary background of convergent evolution for ever-growing molars.
Collapse
Affiliation(s)
- Zachary T. Calamari
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- The Graduate Center, City University of New York, 365 Fifth Ave, New York, NY 10016, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Andrew Song
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- Cornell University, 616 Thurston Ave, Ithaca, NY 14853, USA
| | - Emily Cohen
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- New York University College of Dentistry, 345 E 34th St, New York, NY 10010
| | - Muspika Akter
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Outi Hallikas
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mona M. Christensen
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pengyang Li
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| |
Collapse
|
2
|
Majane AC, Cridland JM, Blair LK, Begun DJ. Evolution and genetics of accessory gland transcriptome divergence between Drosophila melanogaster and D. simulans. Genetics 2024; 227:iyae039. [PMID: 38518250 PMCID: PMC11151936 DOI: 10.1093/genetics/iyae039] [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: 08/27/2023] [Revised: 08/27/2023] [Accepted: 02/15/2024] [Indexed: 03/24/2024] Open
Abstract
Studies of allele-specific expression in interspecific hybrids have provided important insights into gene-regulatory divergence and hybrid incompatibilities. Many such investigations in Drosophila have used transcriptome data from complex mixtures of many tissues or from gonads, however, regulatory divergence may vary widely among species, sexes, and tissues. Thus, we lack sufficiently broad sampling to be confident about the general biological principles of regulatory divergence. Here, we seek to fill some of these gaps in the literature by characterizing regulatory evolution and hybrid misexpression in a somatic male sex organ, the accessory gland, in F1 hybrids between Drosophila melanogaster and D. simulans. The accessory gland produces seminal fluid proteins, which play an important role in male and female fertility and may be subject to adaptive divergence due to male-male or male-female interactions. We find that trans differences are relatively more abundant than cis, in contrast to most of the interspecific hybrid literature, though large effect-size trans differences are rare. Seminal fluid protein genes have significantly elevated levels of expression divergence and tend to be regulated through both cis and trans divergence. We find limited misexpression (over- or underexpression relative to both parents) in this organ compared to most other Drosophila studies. As in previous studies, male-biased genes are overrepresented among misexpressed genes and are much more likely to be underexpressed. ATAC-Seq data show that chromatin accessibility is correlated with expression differences among species and hybrid allele-specific expression. This work identifies unique regulatory evolution and hybrid misexpression properties of the accessory gland and suggests the importance of tissue-specific allele-specific expression studies.
Collapse
Affiliation(s)
- Alex C Majane
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Julie M Cridland
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Logan K Blair
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| |
Collapse
|
3
|
Yu X, Wei P, Zhao S, Chen Z, Li X, Zhang W, Liu C, Yang Y, Li X, Liu X. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau. PLANT CELL REPORTS 2023; 42:879-893. [PMID: 36973418 DOI: 10.1007/s00299-023-03005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
Collapse
Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuqi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinzhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Wencai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China.
| |
Collapse
|
4
|
Ioannidis P, Buer B, Ilias A, Kaforou S, Aivaliotis M, Orfanoudaki G, Douris V, Geibel S, Vontas J, Denecke S. A spatiotemporal atlas of the lepidopteran pest Helicoverpa armigera midgut provides insights into nutrient processing and pH regulation. BMC Genomics 2022; 23:75. [PMID: 35073840 PMCID: PMC8785469 DOI: 10.1186/s12864-021-08274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Caterpillars from the insect order Lepidoptera are some of the most widespread and destructive agricultural pests. Most of their impact is at the larval stage, where the midgut epithelium mediates the digestion and absorption of an astonishing amount of food. Although this tissue has been the subject of frequent investigation in Lepidoptera, a comprehensive expression atlas has yet to be generated. Results Here, we perform RNA-sequencing and proteomics on the gut of the polyphagous pest Helicoverpa armigera across, life stages, diet types, and compartments of the anterior-posterior axis. A striking relationship between the structural homology and expression pattern of a group of sugar transporters was observed in the early larval stages. Further comparisons were made among the spatial compartments of the midgut, which suggested a putative role for vATPases and SLC9 transporters in the generation of alkaline conditions in the H. armigera midgut. Conclusions This comprehensive resource will aid the scientific community in understanding lepidopteran gut physiology in unprecedented resolution. It is hoped that this study advances the understanding of the lepidopteran midgut and also facilitates functional work in this field. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08274-x.
Collapse
|
5
|
Lyu MJA, Gowik U, Kelly S, Covshoff S, Hibberd JM, Sage RF, Ludwig M, Wong GKS, Westhoff P, Zhu XG. The coordination of major events in C 4 photosynthesis evolution in the genus Flaveria. Sci Rep 2021; 11:15618. [PMID: 34341365 PMCID: PMC8329263 DOI: 10.1038/s41598-021-93381-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex traits and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis. We first mapped transcript abundance, protein sequence and morphological features onto the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features; we then predicted the relative changes of ancestral nodes of those features to illustrate the major events during the evolution of C4 photosynthesis. We found that gene expression and protein sequence showed consistent modification patterns in the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed. The greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species. Our results show highly coordinated changes in gene expression, protein sequence and morphological features, which support evolutionary major events during the evolution of C4 metabolism.
Collapse
Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,Department of Medicine and Department of Biological Sciences, The University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
6
|
Jin L, Tang Q, Hu S, Chen Z, Zhou X, Zeng B, Wang Y, He M, Li Y, Gui L, Shen L, Long K, Ma J, Wang X, Chen Z, Jiang Y, Tang G, Zhu L, Liu F, Zhang B, Huang Z, Li G, Li D, Gladyshev VN, Yin J, Gu Y, Li X, Li M. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nat Commun 2021; 12:3715. [PMID: 34140474 PMCID: PMC8211698 DOI: 10.1038/s41467-021-23560-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits. A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
Collapse
Affiliation(s)
- Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Linyuan Shen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fei Liu
- Information and Educational Technology Center, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zhang
- Ya'an Digital Economy Operation Company, Ya'an, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| |
Collapse
|
7
|
Zhong X, Lundberg M, Råberg L. Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species. Genome Biol Evol 2021; 13:6132239. [PMID: 33565592 PMCID: PMC7936018 DOI: 10.1093/gbe/evab023] [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] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.
Collapse
Affiliation(s)
| | | | - Lars Råberg
- Department of Biology, Lund University, Sweden
| |
Collapse
|
8
|
El Taher A, Böhne A, Boileau N, Ronco F, Indermaur A, Widmer L, Salzburger W. Gene expression dynamics during rapid organismal diversification in African cichlid fishes. Nat Ecol Evol 2021; 5:243-250. [PMID: 33230257 PMCID: PMC7610457 DOI: 10.1038/s41559-020-01354-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022]
Abstract
Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of 6 different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts and the subclades of the radiation, indicating different strengths of selection. We found that the noncoding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that-at the per-gene level-the evolution of expression patterns is dominated by stabilizing selection.
Collapse
Affiliation(s)
- Athimed El Taher
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Nicolas Boileau
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Adrian Indermaur
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Lukas Widmer
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
9
|
Ponnanna K, DSouza SM, Amruthavalli C, Ramachandra NB. Allopatric sibling species pair Drosophila nasuta nasuta and Drosophila nasuta albomicans exhibit expression divergence in ovarian transcriptomes. Gene 2020; 777:145189. [PMID: 33035618 DOI: 10.1016/j.gene.2020.145189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 08/18/2020] [Accepted: 09/24/2020] [Indexed: 12/01/2022]
Abstract
Drosophila nasuta nasuta and Drosophila nasuta albomicans represent cross fertile members of the immigrans species group of Drosophila with an allopatric mode of distribution exhibiting characteristic novelties. Illumina sequencing technology and de novo transcriptome assembling strategies were used for the current study. The analysis revealed 8% of the transcriptome to be differentially expressed between the ovaries of these two species, of which 9% was related to female reproduction. The majority of the differentially expressed genes were enriched for genetic information processing pathways, biosynthesis, and metabolism-related pathways. SNPs in D. n. albomicans transcriptome was double in number than in D. n. nasuta and only 5% of these SNPs were fixed. Ka/Ks ratios indicated the lineages were under strong purifying selection. The genes which are differentially expressed are evolving at a similar rate as that of genes with conserved expression. Thus, the current findings provide useful insights on the expression dynamics during incipient species divergence of D. n. nasuta and D. n. albomicans since their divergence time of ~ 0.5 million years.
Collapse
Affiliation(s)
- Koushik Ponnanna
- Department of Studies in Genetics & Genomics, University of Mysore, Mysuru, KA, India.
| | - Stafny M DSouza
- Department of Studies in Genetics & Genomics, University of Mysore, Mysuru, KA, India.
| | - C Amruthavalli
- Department of Studies in Genetics & Genomics, University of Mysore, Mysuru, KA, India
| | - Nallur B Ramachandra
- Department of Studies in Genetics & Genomics, University of Mysore, Mysuru, KA, India.
| |
Collapse
|
10
|
Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun 2020; 11:4459. [PMID: 32900997 PMCID: PMC7479108 DOI: 10.1038/s41467-020-18090-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein-Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.
Collapse
|
11
|
Lian S, Zhou Y, Liu Z, Gong A, Cheng L. The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences. BMC PLANT BIOLOGY 2020; 20:277. [PMID: 32546126 PMCID: PMC7298774 DOI: 10.1186/s12870-020-02460-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences and expression differences have arisen due to selective pressures throughout evolution. A comprehensive investigation of the expression patterns of paralogous gene pairs in response to various stresses and a study of correlations between the expression levels and sequence divergences of the paralogs are needed. RESULTS In this study, we analyzed the expression patterns of paralogous genes under different types of stress and investigated the correlations between the expression levels and sequence divergences of the paralogs. We analyzed the differential expression patterns of the paralogs under four different types of stress (drought, cold, infection, and herbivory) and classified them into three main types according to their expression patterns. We then further analyzed the differential expression patterns under various degrees of stress and constructed corresponding co-expression networks of differentially expressed paralogs and transcription factors. Finally, we investigated the correlations between the expression levels and sequence divergences of the paralogs and identified positive correlations between expression level and sequence divergence. With regard to sequence divergence, we identified correlations between selective pressures and phylogenetic relationships. CONCLUSIONS These results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relationships between expression levels and sequences divergences.
Collapse
Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Andong Gong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Lin Cheng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| |
Collapse
|
12
|
Mota-Martorell N, Jove M, Pradas I, Sanchez I, Gómez J, Naudi A, Barja G, Pamplona R. Low abundance of NDUFV2 and NDUFS4 subunits of the hydrophilic complex I domain and VDAC1 predicts mammalian longevity. Redox Biol 2020; 34:101539. [PMID: 32353747 PMCID: PMC7191849 DOI: 10.1016/j.redox.2020.101539] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 01/14/2023] Open
Abstract
Mitochondrial reactive oxygen species (ROS) production, specifically at complex I (Cx I), has been widely suggested to be one of the determinants of species longevity. The present study follows a comparative approach to analyse complex I in heart tissue from 8 mammalian species with a longevity ranging from 3.5 to 46 years. Gene expression and protein content of selected Cx I subunits were analysed using droplet digital PCR (ddPCR) and western blot, respectively. Our results demonstrate: 1) the existence of species-specific differences in gene expression and protein content of Cx I in relation to longevity; 2) the achievement of a longevity phenotype is associated with low protein abundance of subunits NDUFV2 and NDUFS4 from the matrix hydrophilic domain of Cx I; and 3) long-lived mammals show also lower levels of VDAC (voltage-dependent anion channel) amount. These differences could be associated with the lower mitochondrial ROS production and slower aging rate of long-lived animals and, unexpectedly, with a low content of the mitochondrial permeability transition pore in these species. There are species-specific differences in gene expression and protein content of Cx I. The achievement of a longevity phenotype is associated with low protein abundance of subunits NDUFV2 and NDUFS4 from the matrix hydrophilic domain of Cx I. Long-lived mammals show also lower levels of VDAC (voltage-dependent anion channel) amount. These differences can be causally associated with the aging rate of long-lived animals.
Collapse
Affiliation(s)
- Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Mariona Jove
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Irene Pradas
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Isabel Sanchez
- Proteomics and Genomics Unit, University of Lleida, Lleida, Catalonia, Spain.
| | - José Gómez
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos I, ESCET-Campus de Móstoles, Móstoles, Madrid, Spain.
| | - Alba Naudi
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain.
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| |
Collapse
|
13
|
Turan ZG, Parvizi P, Dönertaş HM, Tung J, Khaitovich P, Somel M. Molecular footprint of Medawar's mutation accumulation process in mammalian aging. Aging Cell 2019; 18:e12965. [PMID: 31062469 PMCID: PMC6612638 DOI: 10.1111/acel.12965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/14/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022] Open
Abstract
Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging‐related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age‐related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up‐regulated during aging. In general, the more often a gene is found up‐regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up‐regulated genes have overlapping functional properties that include responses to age‐associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.
Collapse
Affiliation(s)
- Zeliha Gözde Turan
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Poorya Parvizi
- Department of Biological Sciences Middle East Technical University Ankara Turkey
- Usher Institute of Population Health Sciences and Informatics University of Edinburgh Edinburgh UK
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL‐EBI Wellcome Trust Genome Campus Cambridge UK
| | - Jenny Tung
- Department of Evolutionary Anthropology Duke University Durham North Carolina
- Department of Biology Duke University Durham North Carolina
- Duke Population Research Institute Duke University Durham North Carolina
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration Skolkovo Institute of Science and Technology Moscow Russia
- CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Mehmet Somel
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| |
Collapse
|
14
|
Huminiecki L. Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PLoS One 2019; 14:e0208952. [PMID: 30802244 PMCID: PMC6389290 DOI: 10.1371/journal.pone.0208952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Magic roundabout (ROBO4) is an unusual endothelial-specific paralog of the family of neuronally-expressed axon guidance receptors called roundabouts. Endothelial cells (ECs), whose uninterrupted sheet delimits the lumen of all vertebrate blood vessels and which are absent from invertebrate species, are a vertebrate-specific evolutionary novelty. RESULTS Herein, the evolutionary mechanism of the duplication, retention and divergence of ROBO4 was investigated for the first time. Phylogenetic analyses carried out suggested that ROBO4 is a fast-evolving paralog of ROBO1 formed at the base of vertebrates. The ancestral expression pattern was neuronal. ROBO4 dramatically shifted its expression and became exceptionally specific to ECs. The data-mining of FANTOM5 and ENCODE reveals that ROBO4's endothelial expression arises from a single transcription start site (TSS), conserved in mouse, controlled by a proximal promoter with a complex architecture suggestive of regulatory neo-functionalization. (An analysis of promoter probabilities suggested the architecture was not due to a chance arrangement of TFBSes). Further evidence for the neo-functionalization of ROBO4 comes from the analysis of its protein interactions, the rates of protein evolution, and of positively selected sites. CONCLUSIONS The neo-functionalization model explains why ROBO4 protein acquired new context-specific biological functions in the control of angiogenesis. This endothelial-specific roundabout receptor is an illustrative example of the emergence of an essential vertebrate molecular novelty and an endothelial-specific signaling sub-network through 2R-WGD. The emergence of novel cell types, such as ECs, might be a neglected evolutionary force contributing to the high rate of retention of duplicates post-2R-WGD. Crucially, expression neo-functionalization to evolutionarily novel sites of expression conceptually extends the classical model of neo-functionalization.
Collapse
Affiliation(s)
- Lukasz Huminiecki
- Instytut Genetyki i Hodowli Zwierząt Polskiej Akademii Nauk, Jastrzębiec, Magdalenka, Poland
| |
Collapse
|
15
|
Guillén Y, Casillas S, Ruiz A. Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis. J Hered 2019; 110:92-101. [PMID: 30124907 DOI: 10.1093/jhered/esy041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022] Open
Abstract
Evolutionary rates for protein-coding genes are determined not only by natural selection but also by multiple genomic factors including mutation rates, recombination, gene expression levels, and chromosomal location. To investigate the joint effects of different genomic determinants on protein evolution, we compared the coding sequences of 9017 single-copy orthologs between 2 cactophilic species from the Drosophila subgenus, Drosophila mojavensis and D. buzzatii, whose genomes have been previously sequenced. We assessed the impact of 7 genomic determinants, that is, chromosome type, recombination, chromosomal inversions, expression breadth, expression level, gene length, and the number of exons, on divergence rates of protein-coding genes to understand patterns of evolutionary variation. Integrative analysis of these factors revealed that 1) X-linked and autosomal genes evolve at significantly different rates in agreement with the faster-X hypothesis, 2) genes located on the dot chromosome and pericentromeric regions have higher divergence rates, 3) genes located at chromosomes with more fixed inversions have higher pairwise divergence than those located at nearly collinear chromosomes, and 4) gene expression patterns can be considered the strongest determinant of protein evolution. In addition, the number of exons and protein length had a significant effect on pairwise divergence at synonymous sites. All in all, our results show the relative importance of each genomic factor on the rates of protein evolution and functional constraint in these 2 cactophilic Drosophila species.
Collapse
Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sònia Casillas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,The Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| |
Collapse
|
16
|
Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
Collapse
Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
| |
Collapse
|
17
|
Abril SIM, Costa PG, Bianchini A. Metal accumulation and expression of genes encoding for metallothionein and copper transporters in a chronically exposed wild population of the fish Hyphessobrycon luetkenii. Comp Biochem Physiol C Toxicol Pharmacol 2018; 211:25-31. [PMID: 29783005 DOI: 10.1016/j.cbpc.2018.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 11/17/2022]
Abstract
In the present study, metal (As, Cd, Cu, Fe, Mn, Pb and Zn) accumulation and expression of genes involved in metal metabolism (metallothioneins, ATP7A and CTR1) were evaluated in gills and muscle of the fish Hyphessobrycon luetkenii living in the João Dias creek, a site historically (~1870-1996) contaminated with a metal mixture associated with copper mining (Minas do Camaquã, southern Brazil). Fish were collected in a metal impacted site of the João Dias creek and kept in a cage at this site (PP fish) or translocated to a non-metal impacted reach of this creek (PC fish). Gill metal concentrations and metallothionein gene expression were lower in PC fish than in PP fish at any experimental time (24, 48 and 72 h). In muscle, no significant changes were observed. These findings indicate that metal accumulated in gills of wild fish chronically exposed to the metal mixture are more easily excreted than those accumulated in the muscle. In this case, expression of gene encoding for metallothionein is shown to play a key role in the regulation of metal accumulation in gills of H. luetkenii living in an area historically contaminated with a metal mixture associated with copper mining.
Collapse
Affiliation(s)
- Sandra Isabel Moreno Abril
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900 Rio Grande, RS, Brazil
| | - Patrícia Gomes Costa
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900 Rio Grande, RS, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900 Rio Grande, RS, Brazil.
| |
Collapse
|
18
|
Guschanski K, Warnefors M, Kaessmann H. The evolution of duplicate gene expression in mammalian organs. Genome Res 2017; 27:1461-1474. [PMID: 28743766 PMCID: PMC5580707 DOI: 10.1101/gr.215566.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 07/18/2017] [Indexed: 12/16/2022]
Abstract
Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.
Collapse
Affiliation(s)
- Katerina Guschanski
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, S-75105 Uppsala, Sweden
| | - Maria Warnefors
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| |
Collapse
|
19
|
Schrader L, Helanterä H, Oettler J. Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior. Mol Biol Evol 2017; 34:535-544. [PMID: 27999112 PMCID: PMC5400372 DOI: 10.1093/molbev/msw240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior—a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity.
Collapse
Affiliation(s)
- Lukas Schrader
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jan Oettler
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany
| |
Collapse
|
20
|
Pespeni MH, Ladner JT, Moczek AP. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. J Evol Biol 2017; 30:1644-1657. [PMID: 28379613 DOI: 10.1111/jeb.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/05/2017] [Indexed: 01/20/2023]
Abstract
Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.
Collapse
Affiliation(s)
- M H Pespeni
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| | - J T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - A P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
| |
Collapse
|
21
|
Morandin C, Mikheyev AS, Pedersen JS, Helanterä H. Evolutionary constraints shape caste-specific gene expression across 15 ant species. Evolution 2017; 71:1273-1284. [PMID: 28262920 DOI: 10.1111/evo.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.
Collapse
Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Jes Søe Pedersen
- Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| |
Collapse
|
22
|
Hodgins KA, Yeaman S, Nurkowski KA, Rieseberg LH, Aitken SN. Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers. Mol Biol Evol 2016; 33:1502-16. [PMID: 26873578 DOI: 10.1093/molbev/msw032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers.
Collapse
Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Sam Yeaman
- Department of Botany, University of British Columbia, Vancouver, BC, Canada Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
23
|
Kavembe GD, Franchini P, Irisarri I, Machado-Schiaffino G, Meyer A. Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa. J Mol Evol 2015; 81:90-109. [DOI: 10.1007/s00239-015-9696-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
|
24
|
Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE. High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. J Comp Neurol 2015; 524:288-308. [PMID: 26132897 DOI: 10.1002/cne.23843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/20/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022]
Abstract
The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes.
Collapse
Affiliation(s)
- Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Zhuo-Cheng Hou
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Animal Genetics, China Agricultural University, Beijing, China
| | - Hui Jia
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Christopher Sinkler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Michael McGowen
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, Oregon, 97403
| | - Amy Weckle
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801.,Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois, 61801
| | - Amara B Sugalski
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Lenore Pipes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10021
| | - Domenico L Gatti
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, Michigan, 48201.,Cardiovascular Research Institute, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10021
| | - Chet C Sherwood
- Department of Anthropology and the Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029.,New York Consortium in Evolutionary Primatology, New York, New York, 10024
| | | | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Morris Goodman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Anatomy and Cell Biology, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Derek E Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801.,Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois, 61801
| |
Collapse
|
25
|
Bauernfeind AL, Soderblom EJ, Turner ME, Moseley MA, Ely JJ, Hof PR, Sherwood CC, Wray GA, Babbitt CC. Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees. Genome Biol Evol 2015; 7:2276-88. [PMID: 26163674 PMCID: PMC4558850 DOI: 10.1093/gbe/evv132] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although transcriptomic profiling has become the standard approach for exploring molecular differences in the primate brain, very little is known about how the expression levels of gene transcripts relate to downstream protein abundance. Moreover, it is unknown whether the relationship changes depending on the brain region or species under investigation. We performed high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses on two regions of the human and chimpanzee brain: The anterior cingulate cortex and caudate nucleus. In both brain regions, we found a lower correlation between mRNA and protein expression levels in humans and chimpanzees than has been reported for other tissues and cell types, suggesting that the brain may engage extensive tissue-specific regulation affecting protein abundance. In both species, only a few categories of biological function exhibited strong correlations between mRNA and protein expression levels. These categories included oxidative metabolism and protein synthesis and modification, indicating that the expression levels of mRNA transcripts supporting these biological functions are more predictive of protein expression compared with other functional categories. More generally, however, the two measures of molecular expression provided strikingly divergent perspectives into differential expression between human and chimpanzee brains: mRNA comparisons revealed significant differences in neuronal communication, ion transport, and regulatory processes, whereas protein comparisons indicated differences in perception and cognition, metabolic processes, and organization of the cytoskeleton. Our results highlight the importance of examining protein expression in evolutionary analyses and call for a more thorough understanding of tissue-specific protein expression levels.
Collapse
Affiliation(s)
- Amy L Bauernfeind
- Department of Anatomy and Neurobiology, Washington University Medical School Department of Anthropology, Washington University in St. Louis Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine Center for Genomic and Computational Biology, Duke University
| | - Meredith E Turner
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine Center for Genomic and Computational Biology, Duke University
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine Center for Genomic and Computational Biology, Duke University
| | | | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York New York Consortium in Evolutionary Primatology, New York, New York
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University Department of Biology, Duke University Department of Evolutionary Anthropology, Duke University
| | | |
Collapse
|
26
|
Kryuchkova-Mostacci N, Robinson-Rechavi M. Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PLoS One 2015; 10:e0131673. [PMID: 26121354 PMCID: PMC4488272 DOI: 10.1371/journal.pone.0131673] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/04/2015] [Indexed: 12/23/2022] Open
Abstract
Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.
Collapse
Affiliation(s)
- Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
27
|
De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol 2015; 7:1002-15. [PMID: 25747252 PMCID: PMC4419791 DOI: 10.1093/gbe/evv044] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
Collapse
Affiliation(s)
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Genomics Research Institute, University of Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Sweden Umeå Plant Science Centre, Umeå, Sweden
| |
Collapse
|
28
|
Popadin K, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev S, Lukowski S, Bazykin G, Seplyarskiy V, Ioannidis P, Zdobnov E, Dermitzakis E, Antonarakis S. Gene age predicts the strength of purifying selection acting on gene expression variation in humans. Am J Hum Genet 2014; 95:660-74. [PMID: 25480033 DOI: 10.1016/j.ajhg.2014.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression levels (cis expression quantitative trait loci [cis-eQTLs]) and protein levels (cis protein QTLs [cis-pQTLs]), we determined that young, primate-specific genes are enriched in cis-eQTLs and cis-pQTLs. Compared to cis-eQTLs of old genes originating before the zebrafish divergence, cis-eQTLs of young genes have a higher effect size, are located closer to the transcription start site, are more significant, and tend to influence genes in multiple tissues and populations. These results suggest that the expression constraint of each gene increases throughout its lifespan. We also detected a positive correlation between expression constraints (approximated by cis-eQTL properties) and coding constraints (approximated by Ka/Ks) and observed that this correlation might be driven by gene age. To uncover factors associated with the increase in gene-age-related expression constraints, we demonstrated that gene connectivity, gene involvement in complex regulatory networks, gene haploinsufficiency, and the strength of posttranscriptional regulation increase with gene age. We also observed an increase in heritability of gene expression levels with age, implying a reduction of the environmental component. In summary, we show that gene age shapes key gene properties during evolution and is therefore an important component of genome function.
Collapse
|
29
|
Necsulea A, Kaessmann H. Evolutionary dynamics of coding and non-coding transcriptomes. Nat Rev Genet 2014; 15:734-48. [PMID: 25297727 DOI: 10.1038/nrg3802] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.
Collapse
Affiliation(s)
- Anamaria Necsulea
- Laboratory of Developmental Genomics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| |
Collapse
|
30
|
Helanterä H, Uller T. Neutral and adaptive explanations for an association between caste-biased gene expression and rate of sequence evolution. Front Genet 2014; 5:297. [PMID: 25221570 PMCID: PMC4148897 DOI: 10.3389/fgene.2014.00297] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/08/2014] [Indexed: 12/30/2022] Open
Abstract
The castes of social insects provide outstanding opportunities to address the causes and consequences of evolution of discrete phenotypes, i.e., polymorphisms. Here we focus on recently described patterns of a positive association between the degree of caste-specific gene expression and the rate of sequence evolution. We outline how neutral and adaptive evolution can cause genes that are morph-biased in their expression profiles to exhibit historical signatures of faster or slower sequence evolution compared to unbiased genes. We conclude that evaluation of different hypotheses will benefit from (i) reconstruction of the phylogenetic origin of biased expression and changes in rates of sequence evolution, and (ii) replicated data on gene expression variation within versus between morphs. Although the data are limited at present, we suggest that the observed phylogenetic and intra-population variation in gene expression lends support to the hypothesis that the association between caste-biased expression and rate of sequence evolution largely is a result of neutral processes.
Collapse
Affiliation(s)
- Heikki Helanterä
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of HelsinkiHelsinki, Finland
| | - Tobias Uller
- Department of Zoology, Edward Grey Institute, University of OxfordOxford, UK
- Department of Biology, University of LundSölvegatan, Lund, Sweden
| |
Collapse
|