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
|
Tourmente M, Sansegundo E, Rial E, Roldan ERS. Bioenergetic changes in response to sperm capacitation and two-way metabolic compensation in a new murine model. Cell Mol Life Sci 2023; 80:11. [PMID: 36534181 PMCID: PMC9763147 DOI: 10.1007/s00018-022-04652-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/29/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
The acquisition of fertilizing ability by mammalian spermatozoa, known as "capacitation," includes processes that depend on particular metabolic pathways. This has led to the hypothesis that ATP demands might differ between capacitated and non-capacitated cells. Mouse sperm can produce ATP via OXPHOS and aerobic glycolysis, an advantageous characteristic considering that these cells have to function in the complex and variable environment of the female reproductive tract. Nonetheless, despite evidence showing that both metabolic pathways play a role in events associated with mouse sperm capacitation, there is contradictory evidence regarding changes promoted by capacitation in this species. In addition, the vast majority of studies regarding murine sperm metabolism use Mus musculus laboratory strains as model, thus neglecting the wide diversity of sperm traits of other species of Mus. Focus on closely related species with distinct evolutionary histories, which may be the result of different selective pressures, could shed light on diversity of metabolic processes. Here, we analyzed variations in sperm bioenergetics associated with capacitation in spermatozoa of the steppe mouse, Mus spicilegus, a species with high sperm performance. Furthermore, we compared sperm metabolic traits of this species with similar traits previously characterized in M. musculus. We found that the metabolism of M. spicilegus sperm responded to capacitation in a manner similar to that of M. musculus sperm. However, M. spicilegus sperm showed distinct metabolic features, including the ability to perform cross-pathway metabolic compensation in response to either respiratory or glycolytic inhibition, thus revealing a delicate fine-tuning of its metabolic capacities.
Collapse
Affiliation(s)
- Maximiliano Tourmente
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.
- Centro de Biología Celular y Molecular, Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN - UNC), Universidad Nacional de Córdoba, Córdoba, Argentina.
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (IIByT - CONICET, UNC), Córdoba, Argentina.
| | - Ester Sansegundo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Eduardo Rial
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Eduardo R S Roldan
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.
| |
Collapse
|
3
|
Cryns NG, Lin WC, Motahari N, Krentzman OJ, Chen W, Prounis G, Wilbrecht L. The maturation of exploratory behavior in adolescent Mus spicilegus on two photoperiods. Front Behav Neurosci 2022; 16:988033. [PMID: 36408449 PMCID: PMC9672084 DOI: 10.3389/fnbeh.2022.988033] [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: 07/06/2022] [Accepted: 10/10/2022] [Indexed: 09/08/2024] Open
Abstract
Dispersal from the natal site or familial group is a core milestone of adolescent development in many species. A wild species of mouse, Mus spicilegus, presents an exciting model in which to study adolescent development and dispersal because it shows different life history trajectory depending on season of birth. M. spicilegus born in spring and summer on long days (LD) disperse in the first 3 months of life, while M. spicilegus born on shorter autumnal days (SD) delay dispersal through the wintertime. We were interested in using these mice in a laboratory context to compare age-matched mice with differential motivation to disperse. To first test if we could find a proxy for dispersal related behavior in the laboratory environment, we measured open field and novel object investigation across development in M. spicilegus raised on a LD 12 h:12 h light:dark cycle. We found that between the first and second month of life, distance traveled and time in center of the open field increased significantly with age in M. spicilegus. Robust novel object investigation was observed in all age groups and decreased between the 2nd and 3rd month of life in LD males. Compared to male C57BL/6 mice, male M. spicilegus traveled significantly longer distances in the open field but spent less time in the center of the field. However, when a novel object was placed in the center of the open field, Male M. spicilegus, were significantly more willing to contact and mount it. To test if autumnal photoperiod affects exploratory behavior in M. spicilegus in a laboratory environment, we reared a cohort of M. spicilegus on a SD 10 h:14 h photoperiod and tested their exploratory behavior at P60-70. At this timepoint, we found SD rearing had no effect on open field metrics, but led to reduced novel object investigation. We also observed that in P60-70 males, SD reared M. spicilegus weighed less than LD reared M. spicilegus. These observations establish that SD photoperiod can delay weight gain and blunt some, but not all forms of exploratory behavior in adolescent M. spicilegus.
Collapse
Affiliation(s)
- Noah G. Cryns
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Wan Chen Lin
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Niloofar Motahari
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Oliver J. Krentzman
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Weihang Chen
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, United States
| | - George Prounis
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Linda Wilbrecht
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Psychology, University of California, Berkeley, Berkeley, CA, United States
| |
Collapse
|
4
|
Tsuchiya MTN, Dikow RB, Cassin-Sackett L. First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. Genome Biol Evol 2021; 12:618-625. [PMID: 32277812 PMCID: PMC7250503 DOI: 10.1093/gbe/evaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2020] [Indexed: 12/30/2022] Open
Abstract
Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.
Collapse
Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | | |
Collapse
|
5
|
Nguyen QAT, Hillis D, Katada S, Harris T, Pontrello C, Garland T, Haga-Yamanaka S. Coadaptation of the chemosensory system with voluntary exercise behavior in mice. PLoS One 2020; 15:e0241758. [PMID: 33237909 PMCID: PMC7688120 DOI: 10.1371/journal.pone.0241758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Ethologically relevant chemical senses and behavioral habits are likely to coadapt in response to selection. As olfaction is involved in intrinsically motivated behaviors in mice, we hypothesized that selective breeding for a voluntary behavior would enable us to identify novel roles of the chemosensory system. Voluntary wheel running (VWR) is an intrinsically motivated and naturally rewarding behavior, and even wild mice run on a wheel placed in nature. We have established 4 independent, artificially evolved mouse lines by selectively breeding individuals showing high VWR activity (High Runners; HRs), together with 4 non-selected Control lines, over 88 generations. We found that several sensory receptors in specific receptor clusters were differentially expressed between the vomeronasal organ (VNO) of HRs and Controls. Moreover, one of those clusters contains multiple single-nucleotide polymorphism loci for which the allele frequencies were significantly divergent between the HR and Control lines, i.e., loci that were affected by the selective breeding protocol. These results indicate that the VNO has become genetically differentiated between HR and Control lines during the selective breeding process. Although the role of the vomeronasal chemosensory receptors in VWR activity remains to be determined, the current results suggest that these vomeronasal chemosensory receptors are important quantitative trait loci for voluntary exercise in mice. We propose that olfaction may play an important role in motivation for voluntary exercise in mammals.
Collapse
Affiliation(s)
- Quynh Anh Thi Nguyen
- Neuroscience Graduate Program, University of California Riverside, Riverside, California, United States of America
| | - David Hillis
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, California, United States of America
| | - Sayako Katada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Timothy Harris
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, California, United States of America
| | - Crystal Pontrello
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Theodore Garland
- Neuroscience Graduate Program, University of California Riverside, Riverside, California, United States of America
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, California, United States of America
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, United States of America
| | - Sachiko Haga-Yamanaka
- Neuroscience Graduate Program, University of California Riverside, Riverside, California, United States of America
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, California, United States of America
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|
6
|
Sheehan MJ, Campbell P, Miller CH. Evolutionary patterns of major urinary protein scent signals in house mice and relatives. Mol Ecol 2019; 28:3587-3601. [DOI: 10.1111/mec.15155] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 01/04/2023]
Affiliation(s)
| | - Polly Campbell
- Evolution, Ecology and Organismal Biology University of California – Riverside Riverside CA USA
| | | |
Collapse
|