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Bozlak E, Pokharel K, Weldenegodguad M, Paasivaara A, Stammler F, Røed KH, Kantanen J, Wallner B. Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies. Ecol Evol 2024; 14:e11573. [PMID: 38863721 PMCID: PMC11164974 DOI: 10.1002/ece3.11573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.
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Affiliation(s)
- Elif Bozlak
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
- Vienna Graduate School of Population GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | | | | | - Knut H. Røed
- Department of Preclinical Sciences and PathologyNorwegian University of Life SciencesÅsNorway
| | | | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
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2
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Meier SA, Furrer M, Nowak N, Zenobi R, Sundset MA, Huber R, Brown SA, Wagner G. Uncoupling of behavioral and metabolic 24-h rhythms in reindeer. Curr Biol 2024; 34:1596-1603.e4. [PMID: 38503287 DOI: 10.1016/j.cub.2024.02.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/04/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024]
Abstract
Reindeer in the Arctic seasonally suppress daily circadian patterns of behavior present in most animals.1 In humans and mice, even when all daily behavioral and environmental influences are artificially suppressed, robust endogenous rhythms of metabolism governed by the circadian clock persist and are essential to health.2,3 Disrupted rhythms foster metabolic disorders and weight gain.4 To understand circadian metabolic organization in reindeer, we performed behavioral measurements and untargeted metabolomics from blood plasma samples taken from Eurasian tundra reindeer (Rangifer tarandus tarandus) across 24 h at 2-h intervals in four seasons. Our study confirmed the absence of circadian rhythms of behavior under constant darkness in the Arctic winter and constant daylight in the Arctic summer, as reported by others.1 We detected and measured the intensity of 893 metabolic features in all plasma samples using untargeted ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS). A core group of metabolites (66/893 metabolic features) consistently displayed 24-h rhythmicity. Most metabolites displayed a robust 24-h rhythm in winter and spring but were arrhythmic in summer and fall. Half of all measured metabolites displayed ultradian sleep-wake dependence in summer. Irrespective of the arrhythmic behavior, metabolism is rhythmic (24 h) in seasons of low food availability, potentially favoring energy efficiency. In seasons of food abundance, 24-h rhythmicity in metabolism is drastically reduced, again irrespective of behavioral rhythms, potentially fostering weight gain.
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Affiliation(s)
- Sara A Meier
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Melanie Furrer
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland
| | - Nora Nowak
- Department of Chemistry and Applied Biosciences, Swiss National Technical University (ETH), 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Swiss National Technical University (ETH), 8093 Zurich, Switzerland
| | - Monica A Sundset
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Reto Huber
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland; Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland.
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Gabriela Wagner
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway; Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, 9016 Tromsø, Norway.
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3
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Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024; 33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [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: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.
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Affiliation(s)
- Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Mammals and Birds, Greenland Institute of Natural Resources (GINR), Nuuk, Greenland
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hamish A Burnett
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Brage B Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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4
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Lázaro J, Sochacki J, Ebisuya M. The stem cell zoo for comparative studies of developmental tempo. Curr Opin Genet Dev 2024; 84:102149. [PMID: 38199063 PMCID: PMC10882223 DOI: 10.1016/j.gde.2023.102149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024]
Abstract
The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species. We argue that the stem cell zoo constitutes a powerful platform to perform comparative studies of developmental tempo, as well as to study other forms of biological time control such as species-specific lifespan, heart rate, and circadian clocks.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. https://twitter.com/@JorgeLazaroF
| | - Jaroslaw Sochacki
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany.
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5
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Tong C. Convergent genomics and Arctic adaptation of ruminants. Proc Biol Sci 2024; 291:20232448. [PMID: 38166424 PMCID: PMC10762444 DOI: 10.1098/rspb.2023.2448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 01/04/2024] Open
Affiliation(s)
- Chao Tong
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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6
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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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7
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Yu Z, Zhang EE. Disrupted circadian rhythms in the plateau pika. Trends Neurosci 2023; 46:1005-1007. [PMID: 37802756 DOI: 10.1016/j.tins.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
The plateau pika (Ochotona curzoniae) is the most populous mammal on the 'third pole', the Qinghai-Tibet Plateau, and is presumed to have inhabited the region before the plateau rose up from sea level. Herein we discuss the disrupted circadian rhythm in the plateau pika and the gene polymorphism behind this phenotype, placing these findings in the broader context of circadian rhythms under extreme conditions.
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Affiliation(s)
- Ziqing Yu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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8
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Hazlerigg DG, Appenroth D, Tomotani BM, West AC, Wood SH. Biological timekeeping in polar environments: lessons from terrestrial vertebrates. J Exp Biol 2023; 226:jeb246308. [PMID: 38031958 DOI: 10.1242/jeb.246308] [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] [Indexed: 12/01/2023]
Abstract
The polar regions receive less solar energy than anywhere else on Earth, with the greatest year-round variation in daily light exposure; this produces highly seasonal environments, with short summers and long, cold winters. Polar environments are also characterised by a reduced daily amplitude of solar illumination. This is obvious around the solstices, when the Sun remains continuously above (polar 'day') or below (polar 'night') the horizon. Even at the solstices, however, light levels and spectral composition vary on a diel basis. These features raise interesting questions about polar biological timekeeping from the perspectives of function and causal mechanism. Functionally, to what extent are evolutionary drivers for circadian timekeeping maintained in polar environments, and how does this depend on physiology and life history? Mechanistically, how does polar solar illumination affect core daily or seasonal timekeeping and light entrainment? In birds and mammals, answers to these questions diverge widely between species, depending on physiology and bioenergetic constraints. In the high Arctic, photic cues can maintain circadian synchrony in some species, even in the polar summer. Under these conditions, timer systems may be refined to exploit polar cues. In other instances, temporal organisation may cease to be dominated by the circadian clock. Although the drive for seasonal synchronisation is strong in polar species, reliance on innate long-term (circannual) timer mechanisms varies. This variation reflects differing year-round access to photic cues. Polar chronobiology is a productive area for exploring the adaptive evolution of daily and seasonal timekeeping, with many outstanding areas for further investigation.
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Affiliation(s)
- David G Hazlerigg
- Arctic Seasonal Timekeeping Initiative (ASTI), Arctic chronobiology and physiology research group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø NO-9037, Norway
| | - Daniel Appenroth
- Arctic Seasonal Timekeeping Initiative (ASTI), Arctic chronobiology and physiology research group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø NO-9037, Norway
| | - Barbara M Tomotani
- Arctic Seasonal Timekeeping Initiative (ASTI), Arctic chronobiology and physiology research group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø NO-9037, Norway
| | - Alexander C West
- Arctic Seasonal Timekeeping Initiative (ASTI), Arctic chronobiology and physiology research group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø NO-9037, Norway
| | - Shona H Wood
- Arctic Seasonal Timekeeping Initiative (ASTI), Arctic chronobiology and physiology research group, Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø NO-9037, Norway
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9
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Kamenova S, de Muinck EJ, Veiberg V, Utsi TA, Steyaert SMJG, Albon SD, Loe LE, Trosvik P. Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation. FEMS Microbiol Ecol 2023; 99:fiad157. [PMID: 38031339 DOI: 10.1093/femsec/fiad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.
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Affiliation(s)
- Stefaniya Kamenova
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Departments of Ecology and Natural Resource Management, Norwegian University of Life Sciences, 1433 Ås, Norway
- National Museum of Natural History, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Eric J de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Department of Pharmacy, University of Oslo, 0371 Oslo, Norway
| | - Vebjørn Veiberg
- Norwegian Institute for Nature Research, 7034 Trondheim, Norway
| | - Tove Aagnes Utsi
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, UiT The Arctic University of Norway, 9510 Alta, Norway
| | - Sam M J G Steyaert
- Faculty of Biosciences and Aquaculture, Nord University, 7713 Steinkjer, Norway
| | - Steve D Albon
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, United Kingdom
| | - Leif Egil Loe
- Departments of Ecology and Natural Resource Management, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
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10
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Jiang H, Zhao Z, Yu H, Lin Q, Liu Y. Evolutionary traits and functional roles of chemokines and their receptors in the male pregnancy of the Syngnathidae. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:500-510. [PMID: 38045539 PMCID: PMC10689615 DOI: 10.1007/s42995-023-00205-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/27/2023] [Indexed: 12/05/2023]
Abstract
Vertebrates have developed various modes of reproduction, some of which are found in Teleosts. Over 300 species of the Syngnathidae (seahorses, pipefishes and seadragons) exhibit male pregnancies; the males have specialized brood pouches that provide immune protection, nourishment, and oxygen regulation. Chemokines play a vital role at the mammalian maternal-fetal interface; however, their functions in fish reproduction are unclear. This study revealed the evolutionary traits and potential functions of chemokine genes in 22 oviparous, ovoviviparous, and viviparous fish species through comparative genomic analyses. Our results showed that chemokine gene copy numbers and evolutionary rates vary among species with different modes of reproduction. Syngnathidae lost cxcl13 and cxcr5, which are involved in key receptor-ligand pairs for lymphoid organ development. Notably, Syngnathidae have site-specific mutations in cxcl12b and ccl44, suggesting immune function during gestation. Moreover, transcriptome analysis revealed that chemokine gene expression varies among Syngnathidae species with different types of brood pouches, suggesting adaptive variations in chemokine functions among seahorses and their relatives. Furthermore, challenge experiments on seahorse brood pouches revealed a joint immune function of chemokine genes during male pregnancy. This study provides insights into the evolutionary diversity of chemokine genes associated with different reproductive modes in fish. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00205-x.
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Affiliation(s)
- Han Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- University of Chinese Academy of Sciences, Beijing, 101400 China
| | - Zhanwei Zhao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- University of Chinese Academy of Sciences, Beijing, 101400 China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- University of Chinese Academy of Sciences, Beijing, 101400 China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- University of Chinese Academy of Sciences, Beijing, 101400 China
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11
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Lv W, Sha Y, Liu X, He Y, Hu J, Wang J, Li S, Guo X, Shao P, Zhao F, Li M. Interaction between Rumen Epithelial miRNAs-Microbiota-Metabolites in Response to Cold-Season Nutritional Stress in Tibetan Sheep. Int J Mol Sci 2023; 24:14489. [PMID: 37833936 PMCID: PMC10572940 DOI: 10.3390/ijms241914489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Tibetan sheep are already well adapted to cold season nutrient stress on the Tibetan Plateau. Rumen, an important nutrient for metabolism and as an absorption organ in ruminants, plays a vital role in the cold stress adaptations of Tibetan sheep. Ruminal microbiota also plays an indispensable role in rumen function. In this study, combined multiomics data were utilized to comprehensively analyze the interaction mechanism between rumen epithelial miRNAs and microbiota and their metabolites in Tibetan sheep under nutrient stress in the cold season. A total of 949 miRNAs were identified in the rumen epithelium of both cold and warm seasons. A total of 62 differentially expressed (DE) miRNAs were screened using FC > 1.5 and p value < 0.01, and a total of 20,206 targeted genes were predicted by DE miRNAs. KEGG enrichment analysis revealed that DE miRNA-targeted genes were mainly enriched in axon guidance(ko04360), tight junction(ko04530), inflammatory mediator regulation of TRP channels(ko04750) and metabolism-related pathways. Correlation analysis revealed that rumen microbiota, rumen VFAs and DE miRNAs were all correlated. Further study revealed that the targeted genes of cold and warm season rumen epithelial DE miRNAs were coenriched with differential metabolites of microbiota in glycerophospholipid metabolism (ko00564), apoptosis (ko04210), inflammatory mediator regulation of TRP channels (ko04750), small cell lung cancer (ko05222), and choline metabolism in cancer (ko05231) pathways. There are several interactions between Tibetan sheep rumen epithelial miRNAs, rumen microbiota, and microbial metabolites, mainly through maintaining rumen epithelial barrier function and host homeostasis of choline and cholesterol, improving host immunity, and promoting energy metabolism pathways, thus enabling Tibetan sheep to effectively respond to cold season nutrient stress. The results also suggest that rumen microbiota have coevolved with their hosts to improve the adaptive capacity of Tibetan sheep to cold season nutrient stress, providing a new perspective for the study of cold season nutritional stress adaptation in Tibetan sheep.
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Affiliation(s)
- Weibing Lv
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand;
| | - Jiang Hu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Shaobin Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Xinyu Guo
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Pengyang Shao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Fangfang Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
| | - Mingna Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (Y.S.); (J.H.); (J.W.); (S.L.); (X.G.); (P.S.); (F.Z.); (M.L.)
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12
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Han R, Han L, Zhao X, Wang Q, Xia Y, Li H. Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:470-482. [PMID: 36395998 PMCID: PMC10787017 DOI: 10.1016/j.gpb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.
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Affiliation(s)
- Ruobing Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Xunwu Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Qianghui Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yanling Xia
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Heping Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
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13
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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14
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Li M, Li X, Wu Z, Zhang G, Wang N, Dou M, Liu S, Yang C, Meng G, Sun H, Hvilsom C, Xie G, Li Y, Li ZH, Wang W, Jiang Y, Heller R, Wang Y. Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants. Proc Biol Sci 2023; 290:20230538. [PMID: 37253422 PMCID: PMC10229229 DOI: 10.1098/rspb.2023.0538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
The muskox and reindeer are the only ruminants that have evolved to survive in harsh Arctic environments. However, the genetic basis of this Arctic adaptation remains largely unclear. Here, we compared a de novo assembled muskox genome with reindeer and other ruminant genomes to identify convergent amino acid substitutions, rapidly evolving genes and positively selected genes among the two Arctic ruminants. We found these candidate genes were mainly involved in brown adipose tissue (BAT) thermogenesis and circadian rhythm. Furthermore, by integrating transcriptomic data from goat adipose tissues (white and brown), we demonstrated that muskox and reindeer may have evolved modulating mitochondrion, lipid metabolism and angiogenesis pathways to enhance BAT thermogenesis. In addition, results from co-immunoprecipitation experiments prove that convergent amino acid substitution of the angiogenesis-related gene hypoxia-inducible factor 2alpha (HIF2A), resulting in weakening of its interaction with prolyl hydroxylase domain-containing protein 2 (PHD2), may increase angiogenesis of BAT. Altogether, our work provides new insights into the molecular mechanisms involved in Arctic adaptation.
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Affiliation(s)
- Manman Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Guanghui Zhang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, West Yuanmingyuan Road, Beijing 100193, People's Republic of China
| | - Chentao Yang
- BGI Shenzhen, Shenzhen 518083, People's Republic of China
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hailu Sun
- BGI Shenzhen, Shenzhen 518083, People's Republic of China
| | | | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Zhuo hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Wei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, People's Republic of China
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15
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Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, Pečnerová P, Tikhonov A, Protopopov A, Plotnikov V, Kanellidou F, Nikolskiy P, Mortensen P, Danilov GK, Vartanyan S, Gilbert MTP, Lister AM, Heintzman PD, van der Valk T, Dalén L. Genomics of adaptive evolution in the woolly mammoth. Curr Biol 2023; 33:1753-1764.e4. [PMID: 37030294 DOI: 10.1016/j.cub.2023.03.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
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Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| | - Marianne Dehasque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | | | - Foteini Kanellidou
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway
| | | | - Peter D Heintzman
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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16
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Wang W, Li Z, Xie G, Li X, Wu Z, Li M, Liu A, Xiong Y, Wang Y. Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection. Int J Mol Sci 2023; 24:ijms24021165. [PMID: 36674681 PMCID: PMC9860930 DOI: 10.3390/ijms24021165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Manman Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yan Xiong
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Correspondence:
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17
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Si H, Li S, Nan W, Sang J, Xu C, Li Z. Integrated Transcriptome and Microbiota Reveal the Regulatory Effect of 25-Hydroxyvitamin D Supplementation in Antler Growth of Sika Deer. Animals (Basel) 2022; 12:ani12243497. [PMID: 36552417 PMCID: PMC9774409 DOI: 10.3390/ani12243497] [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: 10/29/2022] [Revised: 11/21/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The level of plasma 25-hydroxyvitamin D (25(OH)D) is associated with the growth of the antler, a fast-growing bone organ of Cervidae. However, the benefits of 25(OH)D supplementation on antler growth and the underlying mechanisms remain unclear. Here, the antler growth profile and transcriptome, plasma parameters, rumen bacteria, and metabolites (volatile fatty acids and amino acids) were determined in sika deer in a 25(OH)D supplementation group (25(OH)D, n = 8) and a control group (Ctrl, n = 8). 25(OH)D supplementation significantly increased the antler weight and growth rate. The levels of IGF-1,25(OH)D and 1,25-dihydroxyvitamin D were significantly higher in the 25(OH)D group than in the Ctrl group, while the levels of LDL-C were lower. The levels of valerate and branched-chain amino acids in the rumen fluid were significantly different between the 25(OH)D and Ctrl groups. The bacterial diversity indices were not significantly different between the two groups. However, the relative abundances of the butyrate-producing bacteria (families Lachnospiraceae and Succinivibrionaceae) and the pyruvate metabolism pathway were higher in the 25(OH)D group. The transcriptomic profile of the antler was significantly different between the 25(OH)D and Ctrl groups, with 356 up- and 668 down-regulated differentially expressed genes (DEGs) in the 25(OH)D group. The up-regulated DEGs were enriched in the proteinaceous extracellular matrix and collagen, while the down-regulated DEGs were enriched in the immune system and lipid metabolism pathways. Overall, these results provide novel insights into the effects of 25(OH)D supplementation on the host metabolism, rumen microbiota, and antler transcriptome of sika deer.
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Affiliation(s)
- Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Songze Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Weixiao Nan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jianan Sang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Chao Xu
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- Correspondence: (C.X.); (Z.L.)
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (C.X.); (Z.L.)
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18
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Foster A, Wight A. Reindeer health and welfare. Vet Rec 2022; 191:453-455. [DOI: 10.1002/vetr.2509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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19
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Trammell EJ, Carlson ML, Reynolds JH, Taylor JJ, Schmidt NM. Ecological integrity and conservation challenges in a rapidly changing Arctic: A call for new approaches in large intact landscapes. AMBIO 2022; 51:2524-2531. [PMID: 35779211 PMCID: PMC9584027 DOI: 10.1007/s13280-022-01756-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/15/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Intactness is a commonly used measure of ecological integrity, especially when evaluating conservation status at the landscape scale. We argue that in the large and relatively unfragmented landscapes of the Arctic and sub-Arctic, intactness provides only partial insight for managers charged with maintaining ecological integrity. A recent landscape assessment suggests that 95% of Alaska shows no measured direct or indirect impacts of human development on the landscape. However, the current exceptionally high levels of intactness in Alaska, and throughout the Arctic and sub-Arctic, do not adequately reflect impacts to the region's ecological integrity caused by indirect stressors, such as a rapidly changing climate and the subsequent loss of the cryosphere. Thus, it can be difficult to measure, and manage, some of the conservation challenges presented by the ecological context of these systems. The dominant drivers of change, and their associated ecological and socioeconomic impacts, vary as systems decline in ecological integrity from very high to high, and to intermediate levels, but this is not well understood in the literature. Arctic and sub-Arctic systems, as well as other large intact areas, provide unique opportunities for conservation planning, but require tools and approaches appropriate to unfragmented landscapes undergoing rapid climate-driven ecological transformation. We conclude with possible directions for developing more appropriate metrics for measuring ecological integrity in these systems.
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Affiliation(s)
- E. Jamie Trammell
- Alaska Center for Conservation Science, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508 USA
- Environmental Science, Policy, & Sustainability, Southern Oregon University, 1250 Siskiyou Blvd., Ashland, OR 97520 USA
| | - Matthew L. Carlson
- Alaska Center for Conservation Science, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508 USA
| | - Joel H. Reynolds
- Climate Change Response Program, U.S. National Park Service, 1201 Oakridge Dr. Suite 200, Fort Collins, CO 80525 USA
| | - Jason J. Taylor
- Aldo Leopold Wilderness Research Institute, USDA Forest Service, Rocky Mountain Research Station, 790 E. Beckwith Ave, Missoula, MT 59801 USA
| | - Niels M. Schmidt
- Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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20
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Pirri F, Ometto L, Fuselli S, Fernandes FAN, Ancona L, Perta N, Di Marino D, Le Bohec C, Zane L, Trucchi E. Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin. Heredity (Edinb) 2022; 129:317-326. [PMID: 36207436 PMCID: PMC9708836 DOI: 10.1038/s41437-022-00564-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 01/20/2023] Open
Abstract
The eco-evolutionary history of penguins is characterised by shifting from temperate to cold environments. Breeding in Antarctica, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, more ecologically similar to its sister species, the King penguin, is still an open question. As the Antarctic colonisation likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the relative quantification of the genomic signatures of selection, unique to each sister species, could answer this question. Applying phylogeny-based selection tests on 7651 orthologous genes, we identified a more pervasive selection shift in the Emperor penguin than in the King penguin, supporting the hypothesis that its extreme cold adaptation is a derived state. Furthermore, among candidate genes under selection, four (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold-adapted homeotherms, like the woolly Mammoth, while other 161 genes can be assigned to biological functions relevant to cold adaptation identified in previous studies. Location and structural effects of TRPM8 substitutions in Emperor and King penguin lineages support their functional role with putative divergent effects on thermal adaptation. We conclude that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.
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Affiliation(s)
- Federica Pirri
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Flávia A N Fernandes
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
- Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000, Strasbourg, France
| | - Lorena Ancona
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Nunzio Perta
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Monaco
| | - Lorenzo Zane
- Department of Biology, University of Padova, Padova, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.
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21
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Liu K, Meng T, Chen Q, Hou G, Wang X, Hu S, Gu X, Li H, Li Y, Xiong C, Cao J. Diurnal rhythm of human semen quality: analysis of large-scale human sperm bank data and timing-controlled laboratory study. Hum Reprod 2022; 37:1727-1738. [PMID: 35690928 PMCID: PMC9340113 DOI: 10.1093/humrep/deac135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION Can we identify diurnal oscillations in human semen parameters as well as peak times of semen quality? SUMMARY ANSWER Human semen parameters show substantial diurnal oscillation, with most parameters reaching a peak between 1100 and 1500 h. WHAT IS KNOWN ALREADY A circadian clock appears to regulate different physiological functions in various organs, but it remains controversial whether diurnal rhythms occur in human semen parameters. STUDY DESIGN, SIZE, DURATION The medical record of a provincial human sperm bank (HSB) with 33 430 semen samples collected between 0800 and 1700 h from 1 March 2010 to 8 July 2015 was used to analyze variation in semen parameters among time points. A laboratory study was conducted to collect semen samples (n = 36) from six volunteers at six time points with identical time intervals (2 days plus 4 h) between 6 June and 8 July in 2019, in order to investigate the diurnal oscillation of semen parameters in vivo, with a strictly controlled abstinence period. Therefore, the sperm bank study with a large sample size and the in vivo study with a strictly controlled abstinence period in a 24-h time window could be compared to describe the diurnal rhythms in human semen parameters. PARTICIPANTS/MATERIALS, SETTING, METHODS Samples were obtained from potential HSB donors and from participants in the laboratory study who were volunteers, recruited by flyers distributed in the community. Total sperm count, sperm concentration, semen volume, progressive motility and total motility were assessed using computer-aided sperm analysis. In addition, sperm chromatin integrity parameters (DNA fragmentation index and high DNA stainability) were assessed by the sperm chromatin structure assay, and sperm viability was measured with flow cytometry in the laboratory study. MAIN RESULTS AND THE ROLE OF CHANCE The 33 430 samples from the HSB showed a temporal variation in total sperm count, sperm concentration, semen volume, progressive motility and total motility (all P < 0.001) between 0800 and 1700 h. Consequently, the eligibility of semen samples for use in ART, based on bank standards, fluctuated with time point. Each hour earlier/later than 1100 h was associated with 1.14-fold risk of ineligibility. Similarly, the 36 samples taken during the 24-h time window showed diurnal oscillation. With the pre-collection abstinence period strictly controlled, most semen parameters reached the most favorable level between 1100 and 1500 h. LIMITATIONS, REASONS FOR CAUTION Some of the possible confounding factors, such as energy intake, which might influence semen quality or diurnal rhythms, were not adjusted for in the analyses. In addition, the findings should be considered with caution because the study was conducted in a specific population, time and place, while the timing of oscillations could differ with changing conditions. WIDER IMPLICATIONS OF THE FINDINGS The findings could help us to estimate semen quality more precisely and to obtain higher quality sperm for use in ART and in natural conception. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the National Natural Science Foundation of China (81871208) and National Key R&D Program of China (2017YFC1002001). There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
| | | | | | - Guizhong Hou
- Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China
- Institute for Vaccine Clinical Research, Hebei Province Center for Disease Control and Prevention, Hebei, China
| | - Xiaogang Wang
- Department of Chemical Defense Medicine, School of Military Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Siheng Hu
- Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
| | - Xiuli Gu
- Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
| | - Honggang Li
- Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
| | - Yuyan Li
- Reproductive Medical Center, First Affiliated Hospital of Third Military Medical University (Army Medical University), Chongqing, China
| | - Chengliang Xiong
- Correspondence address. Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China. E-mail: (J.C.); Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430000, China. E-mail: (C.X.)
| | - Jia Cao
- Correspondence address. Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China. E-mail: (J.C.); Hubei Province Human Sperm Bank, Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430000, China. E-mail: (C.X.)
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22
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Xing X, Ai C, Wang T, Li Y, Liu H, Hu P, Wang G, Liu H, Wang H, Zhang R, Zheng J, Wang X, Wang L, Chang Y, Qian Q, Yu J, Tang L, Wu S, Shao X, Li A, Cui P, Zhan W, Zhao S, Wu Z, Shao X, Dong Y, Rong M, Tan Y, Cui X, Chang S, Song X, Yang T, Sun L, Ju Y, Zhao P, Fan H, Liu Y, Wang X, Yang W, Yang M, Wei T, Song S, Xu J, Yue Z, Liang Q, Li C, Ruan J, Yang F. The first high-quality reference genome of sika deer provides insights for high-tannin adaptation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00075-4. [PMID: 35718271 PMCID: PMC10372904 DOI: 10.1016/j.gpb.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
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Affiliation(s)
- Xiumei Xing
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Cheng Ai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Tianjiao Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yang Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huitao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pengfei Hu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Guiwu Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huamiao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Hongliang Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ranran Zhang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Junjun Zheng
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lei Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jinghua Yu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lixin Tang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shigang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiujuan Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Alun Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei Zhan
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Sheng Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhichao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiqun Shao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yimeng Dong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Rong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yihong Tan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xuezhe Cui
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shuzhuo Chang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xingchao Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tongao Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Limin Sun
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yan Ju
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pei Zhao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huanhuan Fan
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ying Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xinhui Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Wanyun Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tao Wei
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shanshan Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Jiaping Xu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Zhigang Yue
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Chunyi Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Fuhe Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
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23
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Ba H, Chen M, Li C. Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae. Front Genet 2022; 13:878078. [PMID: 35664330 PMCID: PMC9157503 DOI: 10.3389/fgene.2022.878078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Antlers constitute an interesting model for basic research in regenerative biology. Despite decades of being studied, much is still unknown about the genes related to antler development. Here, we utilized both the genome and antlerogenic periosteum (AP) transcriptome data of four deer species to reveal antler-related genes through cross-species comparative analysis. The results showed that the global gene expression pattern matches the status of antler phenotypes, supporting the fact that the genes expressed in the AP may be related to antler phenotypes. The upregulated genes of the AP in three-antlered deer showed evidence of co-expression, and their protein sequences were highly conserved. These genes were growth related and likely participated in antler development. In contrast, the upregulated genes in antler-less deer (Chinese water deer) were involved mainly in organismal death and growth failure, possibly related to the loss of antlers during evolution. Overall, this study demonstrates that the co-expressed genes in antlered deer may regulate antler development.
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Affiliation(s)
- Hengxing Ba
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.,Jilin Provincial Key Laboratory of Deer Antler Biology, Changchun, China
| | - Min Chen
- School of Life Sciences, Institute of Eco-Chongming (IEC), East China Normal University, Shanghai, China.,Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai Science and Technology Committee, Shanghai, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China.,College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China.,Jilin Provincial Key Laboratory of Deer Antler Biology, Changchun, China
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24
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Liu N, Tian H, Yu Z, Zhao H, Li W, Sang D, Lin K, Cui Y, Liao M, Xu Z, Chen C, Guo Y, Wang Y, Huang HW, Wang J, Zhang H, Wu W, Huang H, Lv S, Guo Z, Wang W, Zheng S, Wang F, Zhang Y, Cai T, Zhang EE. A highland-adaptation mutation of the Epas1 protein increases its stability and disrupts the circadian clock in the plateau pika. Cell Rep 2022; 39:110816. [PMID: 35584682 DOI: 10.1016/j.celrep.2022.110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/07/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) harbors hundreds of species well adapted to its extreme conditions, including its low-oxygen (hypoxic) atmosphere. Here, we show that the plateau pika-a keystone mammal of the QTP-lacks robust circadian rhythms. The major form of the plateau pika Epas1 protein includes a 24-residue insert caused by a point mutation at the 5' juncture site of Intron14 and is more stable than other mammalian orthologs. Biochemical studies reveal that an Epas1-Bmal1 complex with lower trans-activation activity occupies the E1/E2 motifs at the promoter of the core-clock gene Per2, thus explaining how an Epas1 mutation-selected in the hypoxic conditions of the QTP-disrupts the molecular clockwork. Importantly, experiments with hypoxic chambers show that mice expressing the plateau pika Epas1 ortholog in their suprachiasmatic nucleus have dysregulated central clocks, and pika Epas1 knockin mice reared in hypoxic conditions exhibit dramatically reduced heart damage compared with wild-type animals.
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Affiliation(s)
- Na Liu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, School of Life Sciences, Hubei Normal University, Huangshi, Hubei Province 435002, China
| | - Hongni Tian
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China; Department of Neurosurgery, Xinqiao Hospital, Chongqing 400038, China
| | - Ziqing Yu
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Haijiao Zhao
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China
| | - Di Sang
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Keteng Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yilin Cui
- National Institute of Biological Sciences, Beijing 102206, China; Neuroscience Program, Smith College, Northampton, MA 01063, USA
| | - Meimei Liao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhancong Xu
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Chen Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ying Guo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yibing Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jiawen Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China; Department of Pathology, Henan Cancer Hospital, Zhengzhou, Henan Province 450008, China
| | - Wei Wu
- Department of Neurology, The Second Affiliated Hospital of Nanchang University Medical School, Nanchang, Jiangxi Province 330006, China
| | - He Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Shengqing Lv
- Department of Neurosurgery, Xinqiao Hospital, Chongqing 400038, China
| | | | - Wei Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai Province 810008, China.
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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25
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Liu S, Chen H, Ouyang J, Huang M, Zhang H, Zheng S, Xi S, Tang H, Gao Y, Xiong Y, Cheng D, Chen K, Liu B, Li W, Ren J, Yan X, Mao H. A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. Gigascience 2022; 11:6564124. [PMID: 35383847 PMCID: PMC8985102 DOI: 10.1093/gigascience/giac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/15/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022] Open
Abstract
Background The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl. Results A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl. Conclusions This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.
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Affiliation(s)
- Shaojuan Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Min Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hui Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sumei Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Suwang Xi
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongbo Tang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yuren Gao
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Di Cheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kaifeng Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bingbing Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen 361021, China
| | - Jun Ren
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
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Zhen Y, Ge L, Xu Q, Hu L, Wei W, Huang J, Loor JJ, Yang Q, Wang M, Zhou P. Normal Light-Dark and Short-Light Cycles Regulate Intestinal Inflammation, Circulating Short-chain Fatty Acids and Gut Microbiota in Period2 Gene Knockout Mice. Front Immunol 2022; 13:848248. [PMID: 35371053 PMCID: PMC8971677 DOI: 10.3389/fimmu.2022.848248] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 01/20/2023] Open
Abstract
Regular environmental light–dark (LD) cycle-regulated period circadian clock 2 (Per2) gene expression is essential for circadian oscillation, nutrient metabolism, and intestinal microbiota balance. Herein, we combined environmental LD cycles with Per2 gene knockout to investigate how LD cycles mediate Per2 expression to regulate colonic and cecal inflammatory and barrier functions, microbiome, and short-chain fatty acids (SCFAs) in the circulation. Mice were divided into knockout (KO) and wild type (CON) under normal light–dark cycle (NLD) and short-light (SL) cycle for 2 weeks after 4 weeks of adaptation. The concentrations of SCFAs in the serum and large intestine, the colonic and cecal epithelial circadian rhythm, SCFAs transporter, inflammatory and barrier-related genes, and Illumina 16S rRNA sequencing were measured after euthanasia during 10:00–12:00. KO decreased the feeding frequency at 0:00–2:00 but increased at 12:00–14:00 both under NLD and SL. KO upregulated the expression of Per1 and Rev-erbα in the colon and cecum, while it downregulated Clock and Bmal1. In terms of inflammatory and barrier functions, KO increased the expression of Tnf-α, Tlr2, and Nf-κb p65 in the colon and cecum, while it decreased Claudin and Occludin-1. KO decreased the concentrations of total SCFAs and acetate in the colon and cecum, but it increased butyrate, while it had no impact on SCFAs in the serum. KO increased the SCFAs transporter because of the upregulation of Nhe1, Nhe3, and Mct4. Sequencing data revealed that KO improved bacteria α-diversity and increased Lachnospiraceae and Ruminococcaceae abundance, while it downregulated Erysipelatoclostridium, Prevotellaceae UCG_001, Olsenella, and Christensenellaceae R-7 under NLD in KO mice. Most of the differential bacterial genus were enriched in amino acid and carbohydrate metabolism pathways. Overall, Per2 knockout altered circadian oscillation in the large intestine, KO improved intestinal microbiota diversity, the increase in Clostridiales abundance led to the reduction in SCFAs in the circulation, concentrations of total SCFAs and acetate decreased, while butyrate increased and SCFAs transport was enhanced. These alterations may potentially lead to inflammation of the large intestine. Short-light treatment had minor impact on intestinal microbiome and metabolism.
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Affiliation(s)
- Yongkang Zhen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiaoyun Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liangyu Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Wenjun Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiantao Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan J. Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Qingyong Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, China
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, China
- *Correspondence: Mengzhi Wang, ; Ping Zhou,
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, China
- *Correspondence: Mengzhi Wang, ; Ping Zhou,
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Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Watters M, Musiani M. Selection of both habitat and genes in specialized and endangered caribou. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36. [PMID: 35146809 DOI: 10.1111/cobi.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Genetic mechanisms determining habitat selection and specialization of individuals within species have been hypothesized, but not tested at the appropriate individual level in nature. In this work, we analyzed habitat selection for 139 GPS-collared caribou belonging to three declining ecotypes sampled throughout Northwestern Canada. We used Resource Selection Functions (RSFs) comparing resources at used and available locations. We found that the three caribou ecotypes differed in their use of habitat suggesting specialization. On expected grounds, we also found differences in habitat selection between summer and winter, but also, originally, among the individuals within an ecotype. We next obtained Single Nucleotide Polymorphisms (SNPs) for the same caribou individuals, we detected those associated to habitat selection, and then identified genes linked to these SNPs. These genes had functions related in other organisms to habitat and dietary specializations, and climatic adaptations. We therefore suggest that individual variation in habitat selection was based on genotypic variation in the SNPs of individual caribou, indicating that genetic forces underlie habitat and diet selection in the species. We also suggest that the associations between habitat and genes that we detected may lead to lack of resilience in the species, thus contributing to caribou endangerment. Our work emphasizes that similar mechanisms may exist for other specialized, endangered species. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Montana, MT, 59812, USA
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Y1A 2C6, Canada
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, 4999 98 Ave., Edmonton, AB, T6B 2×3, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, AB, T8V 6J4, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC, V9T 6J 9, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - Megan Watters
- Land and Resource Specialist, 300 - 10003 110th Avenue Fort, St. John, BC, V1J 6M7, Canada
| | - Marco Musiani
- Dept. of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, AB, T2N 1N4, Canada
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28
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Song J, Zheng H, Xue J, Liu J, Sun Q, Yang W, Liu F, Xiang X, He K, Chen Y, Cheng J, Li W, Jin J, Brosius J, Deng C. GPR15-C10ORF99 functional pairing initiates colonic Treg homing in amniotes. EMBO Rep 2021; 23:e53246. [PMID: 34939731 PMCID: PMC8892231 DOI: 10.15252/embr.202153246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023] Open
Abstract
Regulatory T lymphocyte (Treg) homing reactions mediated by G protein‐coupled receptor (GPCR)–ligand interactions play a central role in maintaining intestinal immune homeostasis by restraining inappropriate immune responses in the gastrointestinal tract. However, the origin of Treg homing to the colon remains mysterious. Here, we report that the C10ORF99 peptide (also known as CPR15L and AP57), a cognate ligand of GPR15 that controls Treg homing to the colon, originates from a duplication of the flanking CDHR1 gene and is functionally paired with GPR15 in amniotes. Evolutionary analysis and experimental data indicate that the GPR15–C10ORF99 pair is functionally conserved to mediate colonic Treg homing in amniotes and their expression patterns are positively correlated with herbivore diet in the colon. With the first herbivorous diet in early amniotes, a new biological process (herbivorous diet short‐chain fatty acid‐C10ORF99/GPR15‐induced Treg homing colon immune homeostasis) emerged, and we propose an evolutionary model whereby GPR15–C10ORF99 functional pairing has initiated the first colonic Treg homing reaction in amniotes. Our findings also highlight that GPCR–ligand pairing leads to physiological adaptation during vertebrate evolution.
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Affiliation(s)
- Jingjing Song
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Huaping Zheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingwen Xue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jian Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Sun
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Fang Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiangyin Xiang
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Kai He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Younan Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Jin
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Juergen Brosius
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Deng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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29
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Fu W, Wang R, Nanaei HA, Wang J, Hu D, Jiang Y. RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. Nucleic Acids Res 2021; 50:D1091-D1099. [PMID: 34643708 PMCID: PMC8728256 DOI: 10.1093/nar/gkab887] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.
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Affiliation(s)
- Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
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30
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Weldenegodguad M, Pokharel K, Niiranen L, Soppela P, Ammosov I, Honkatukia M, Lindeberg H, Peippo J, Reilas T, Mazzullo N, Mäkelä KA, Nyman T, Tervahauta A, Herzig KH, Stammler F, Kantanen J. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun Biol 2021; 4:1170. [PMID: 34620965 PMCID: PMC8497613 DOI: 10.1038/s42003-021-02703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.
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Affiliation(s)
- Melak Weldenegodguad
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kisun Pokharel
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Laura Niiranen
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Päivi Soppela
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, Yakutsk, The Sakha Republic (Yakutia) Russia
| | | | - Heli Lindeberg
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Maaninka, Finland
| | - Jaana Peippo
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,NordGen—Nordic Genetic Resource Center, Ås, Norway
| | - Tiina Reilas
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Nuccio Mazzullo
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Kari A. Mäkelä
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- grid.454322.60000 0004 4910 9859Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Arja Tervahauta
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Karl-Heinz Herzig
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Medical Research Center, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.412326.00000 0004 4685 4917Oulu University Hospital, Oulu, Finland ,grid.22254.330000 0001 2205 0971Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Florian Stammler
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
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31
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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32
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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33
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Dong Z, Coates D. Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration. J Proteome Res 2021; 20:2167-2181. [PMID: 33769828 DOI: 10.1021/acs.jproteome.1c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.
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Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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34
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Post-Translational Protein Deimination Signatures in Plasma and Plasma EVs of Reindeer ( Rangifer tarandus). BIOLOGY 2021; 10:biology10030222. [PMID: 33805829 PMCID: PMC7998281 DOI: 10.3390/biology10030222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Reindeer are an important wild and domesticated species of the Arctic, Northern Europe, Siberia and North America. As reindeer have developed various strategies to adapt to extreme environments, this makes them an interesting species for studies into diversity of immune and metabolic functions in the animal kingdom. Importantly, while reindeer carry natural infections caused by viruses (including coronaviruses), bacteria and parasites, they can also act as carriers for transmitting such diseases to other animals and humans, so called zoonosis. Reindeer are also affected by chronic wasting disease, a neuronal disease caused by prions, similar to scrapie in sheep, mad cows disease in cattle and Creutzfeldt-Jakob disease in humans. The current study assessed a specific protein modification called deimination/citrullination, which can change how proteins function and allow them to take on different roles in health and disease processes. Profiling of deiminated proteins in reindeer showed that many important pathways for immune defenses, prion diseases and metabolism are enriched in deiminated proteins, both in plasma, as well as in plasma extracellular vesicles. This study provides a platform for the development of novel biomarkers to assess wild life health status and factors relating to zoonotic disease. Abstract The reindeer (caribou) Rangifer tarandus is a Cervidae in the order Artiodactyla. Reindeer are sedentary and migratory populations with circumpolar distribution in the Arctic, Northern Europe, Siberia and North America. Reindeer are an important wild and domesticated species, and have developed various adaptive strategies to extreme environments. Importantly, deer have also been identified to be putative zoonotic carriers, including for parasites, prions and coronavirus. Therefore, novel insights into immune-related markers are of considerable interest. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family which causes post-translational protein deimination by converting arginine into citrulline in target proteins. This affects protein function in health and disease. Extracellular vesicles (EVs) participate in cellular communication, in physiological and pathological processes, via transfer of cargo material, and their release is partly regulated by PADs. This study assessed deiminated protein and EV profile signatures in plasma from sixteen healthy wild female reindeer, collected in Iceland during screening for parasites and chronic wasting disease. Reindeer plasma EV profiles showed a poly-dispersed distribution from 30 to 400 nm and were positive for phylogenetically conserved EV-specific markers. Deiminated proteins were isolated from whole plasma and plasma EVs, identified by proteomic analysis and protein interaction networks assessed by KEGG and GO analysis. This revealed a large number of deimination-enriched pathways for immunity and metabolism, with some differences between whole plasma and EVs. While shared KEGG pathways for whole plasma and plasma EVs included complement and coagulation pathways, KEGG pathways specific for EVs were for protein digestion and absorption, platelet activation, amoebiasis, the AGE–RAGE signaling pathway in diabetic complications, ECM receptor interaction, the relaxin signaling pathway and the estrogen signaling pathway. KEGG pathways specific for whole plasma were pertussis, ferroptosis, SLE, thyroid hormone synthesis, phagosome, Staphylococcus aureus infection, vitamin digestion and absorption, and prion disease. Further differences were also found between molecular function and biological processes GO pathways when comparing functional STRING networks for deiminated proteins in EVs, compared with deiminated proteins in whole plasma. This study highlights deiminated proteins and EVs as candidate biomarkers for reindeer health and may provide information on regulation of immune pathways in physiological and pathological processes, including neurodegenerative (prion) disease and zoonosis.
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Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment. Animals (Basel) 2020; 10:ani10112181. [PMID: 33266380 PMCID: PMC7700370 DOI: 10.3390/ani10112181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The Nubian ibex is a wild relative of the domestic goat found in hot deserts of Northern Africa and Arabia. The domestic goat is an important livestock species that is mainly found in arid and semi-arid regions of Africa and Asia. The Nubian ibex is well adapted to challenging environments in hot deserts characterized by high diurnal temperatures, intense solar radiation, and scarce water resources. It is therefore important to understand the genetic basis of its adaptation for scientific and economic importance. To identify genes with adaptive traits, the Nubian ibex genome was sequenced and compared with that of related mammals. We identified twenty-five genes under selection in the Nubian ibex that play diverse biological roles such as immune response, visual development, signal transduction, and reproduction. Three other genes under adaptive evolution involved in protective functions of the skin against damaging solar radiation in the desert were identified in Nubian ibex genome. Our finding provides valuable genomic insights into the adaptation of Nubian ibex to desert environments. The genomic information generated in this study can be used in developing appropriate breeding programs aimed at enhancing adaptation of local goats to less favorable habitats in response to changing climates. Abstract The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana.
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Brealey JC, Leitão HG, van der Valk T, Xu W, Bougiouri K, Dalén L, Guschanski K. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. Mol Biol Evol 2020; 37:3003-3022. [PMID: 32467975 PMCID: PMC7530607 DOI: 10.1093/molbev/msaa135] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
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Affiliation(s)
- Jaelle C Brealey
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrique G Leitão
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Wenbo Xu
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Katia Bougiouri
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Appenroth D, Melum VJ, West AC, Dardente H, Hazlerigg DG, Wagner GC. Photoperiodic induction without light-mediated circadian entrainment in a High Arctic resident bird. J Exp Biol 2020; 223:jeb220699. [PMID: 32587064 DOI: 10.1242/jeb.220699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/19/2020] [Indexed: 01/27/2023]
Abstract
Organisms use changes in photoperiod to anticipate and exploit favourable conditions in a seasonal environment. While species living at temperate latitudes receive day length information as a year-round input, species living in the Arctic may spend as much as two-thirds of the year without experiencing dawn or dusk. This suggests that specialised mechanisms may be required to maintain seasonal synchrony in polar regions. Svalbard ptarmigan (Lagopus muta hyperborea) are resident at 74-81°N latitude. They spend winter in constant darkness (DD) and summer in constant light (LL); extreme photoperiodic conditions under which they do not display overt circadian rhythms. Here, we explored how Arctic adaptation in circadian biology affects photoperiodic time measurement in captive Svalbard ptarmigan. For this purpose, DD-adapted birds, showing no circadian behaviour, either remained in prolonged DD, were transferred into a simulated natural photoperiod (SNP) or were transferred directly into LL. Birds transferred from DD to LL exhibited a strong photoperiodic response in terms of activation of the hypothalamic thyrotropin-mediated photoperiodic response pathway. This was assayed through expression of the Eya3, Tshβ and deiodinase genes, as well as gonadal development. While transfer to SNP established synchronous diurnal activity patterns, activity in birds transferred from DD to LL showed no evidence of circadian rhythmicity. These data show that the Svalbard ptarmigan does not require circadian entrainment to develop a photoperiodic response involving conserved molecular elements found in temperate species. Further studies are required to define how exactly Arctic adaptation modifies seasonal timer mechanisms.
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Affiliation(s)
- Daniel Appenroth
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Vebjørn J Melum
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Alexander C West
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Hugues Dardente
- Physiologie de la Reproduction et des Comportements, INRA, CNRS, IFCE, Université de Tours, 37380 Nouzilly, France
| | - David G Hazlerigg
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
| | - Gabriela C Wagner
- Arctic Chronobiology and Physiology, University of Tromsø, 9019 Tromsø, Norway
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Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Sci Rep 2020; 10:8980. [PMID: 32488117 PMCID: PMC7265531 DOI: 10.1038/s41598-020-65487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
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Affiliation(s)
- Melak Weldenegodguad
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70201, Kuopio, Finland
| | - Kisun Pokharel
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Mervi Honkatukia
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Nordic Genetic Resource Centre - NordGen, c/o NMBU - Biovit Box 5003, Ås, NO-1432, Norway
| | - Jaana Peippo
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Tiina Reilas
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, P.O.Box 369 Centrum, 0102, Oslo, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland.
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Nasoori A. Formation, structure, and function of extra-skeletal bones in mammals. Biol Rev Camb Philos Soc 2020; 95:986-1019. [PMID: 32338826 DOI: 10.1111/brv.12597] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 03/07/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
This review describes the formation, structure, and function of bony compartments in antlers, horns, ossicones, osteoderm and the os penis/os clitoris (collectively referred to herein as AHOOO structures) in extant mammals. AHOOOs are extra-skeletal bones that originate from subcutaneous (dermal) tissues in a wide variety of mammals, and this review elaborates on the co-development of the bone and skin in these structures. During foetal stages, primordial cells for the bony compartments arise in subcutaneous tissues. The epithelial-mesenchymal transition is assumed to play a key role in the differentiation of bone, cartilage, skin and other tissues in AHOOO structures. AHOOO ossification takes place after skeletal bone formation, and may depend on sexual maturity. Skin keratinization occurs in tandem with ossification and may be under the control of androgens. Both endochondral and intramembranous ossification participate in bony compartment formation. There is variation in gradients of density in different AHOOO structures. These gradients, which vary according to function and species, primarily reduce mechanical stress. Anchorage of AHOOOs to their surrounding tissues fortifies these structures and is accomplished by bone-bone fusion and Sharpey fibres. The presence of the integument is essential for the protection and function of the bony compartments. Three major functions can be attributed to AHOOOs: mechanical, visual, and thermoregulatory. This review provides the first extensive comparative description of the skeletal and integumentary systems of AHOOOs in a variety of mammals.
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Affiliation(s)
- Alireza Nasoori
- School of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
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Bi X, Zhai J, Xia Y, Li H. Analysis of genetic information from the antlers of Rangifer tarandus (reindeer) at the rapid growth stage. PLoS One 2020; 15:e0230168. [PMID: 32168333 PMCID: PMC7069613 DOI: 10.1371/journal.pone.0230168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/21/2020] [Indexed: 01/22/2023] Open
Abstract
Reindeer is the only deer species in which both males and females regularly grow antlers, providing an excellent model for studying the rapid growth and annual regeneration of antlers. The study of genetic information from reindeer is the basis for revealing the unique mechanism of antler growth. In the present study, we obtained 18.86 GB of clean reads, which were assembled to obtain 94,575 unigenes (average length: 704.69). Among these reads, 30,980 sequences were identified by searching a database of known proteins and then annotated with Gene Ontology (GO) terms, Clusters of Orthologous Groups (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. All 7,480 simple sequence repeats (SSRs) were detected. A total of 84,435 and 82,226 high-quality single-nucleotide polymorphisms (SNPs) were identified in male and female reindeer, respectively. We identified 31 genes that were highly expressed in reindeer antlers. These genes regulate cell activities that are closely associated with the process of rapid tissue growth. Our results provide a basis for studying reindeer antlers and for further studying the molecular genetics, population genetics, and functional genomics of reindeer.
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Affiliation(s)
- Xiaodan Bi
- College of Wildlife and Protected Area, Northeast Forestry University, Xiangfang District, China
- College of Chemistry and Life Science, Chifeng University, Hongshan District, China
| | - Jiancheng Zhai
- College of Wildlife and Protected Area, Northeast Forestry University, Xiangfang District, China
- School of Earth Sciences, East China University of Technology, China
| | - Yanling Xia
- College of Wildlife and Protected Area, Northeast Forestry University, Xiangfang District, China
- School of Earth Sciences, East China University of Technology, China
| | - Heping Li
- College of Wildlife and Protected Area, Northeast Forestry University, Xiangfang District, China
- * E-mail:
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Abstract
Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.
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Affiliation(s)
- Bao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
| | - Le Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China, E-mail:chen_
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:.,Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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Bertolini E, Schubert FK, Zanini D, Sehadová H, Helfrich-Förster C, Menegazzi P. Life at High Latitudes Does Not Require Circadian Behavioral Rhythmicity under Constant Darkness. Curr Biol 2019; 29:3928-3936.e3. [PMID: 31679928 DOI: 10.1016/j.cub.2019.09.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/13/2019] [Accepted: 09/12/2019] [Indexed: 01/08/2023]
Abstract
Nearly all organisms evolved endogenous self-sustained timekeeping mechanisms to track and anticipate cyclic changes in the environment. Circadian clocks, with a periodicity of about 24 h, allow animals to adapt to day-night cycles. Biological clocks are highly adaptive, but strong behavioral rhythms might be a disadvantage for adaptation to weakly rhythmic environments such as polar areas [1, 2]. Several high-latitude species, including Drosophila species, were found to be highly arrhythmic under constant conditions [3-6]. Furthermore, Drosophila species from subarctic regions can extend evening activity until dusk under long days. These traits depend on the clock network neurochemistry, and we previously proposed that high-latitude Drosophila species evolved specific clock adaptations to colonize polar regions [5, 7, 8]. We broadened our analysis to 3 species of the Chymomyza genus, which diverged circa 5 million years before the Drosophila radiation [9] and colonized both low and high latitudes [10, 11]. C. costata, pararufithorax, and procnemis, independently of their latitude of origin, possess the clock neuronal network of low-latitude Drosophila species, and their locomotor activity does not track dusk under long photoperiods. Nevertheless, the high-latitude C. costata becomes arrhythmic under constant darkness (DD), whereas the two low-latitude species remain rhythmic. Different mechanisms are behind the arrhythmicity in DD of C. costata and the high-latitude Drosophila ezoana, suggesting that the ability to maintain behavioral rhythms has been lost more than once during drosophilids' evolution and that it might indeed be an evolutionary adaptation for life at high latitudes.
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Affiliation(s)
- Enrico Bertolini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, 97074 Würzburg, Germany
| | - Frank K Schubert
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, 97074 Würzburg, Germany
| | - Damiano Zanini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, 97074 Würzburg, Germany
| | - Hana Sehadová
- Faculty of Science, Biology Centre of the Czech Academy of Sciences, Institute of Entomology and University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, 97074 Würzburg, Germany
| | - Pamela Menegazzi
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, 97074 Würzburg, Germany.
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Affiliation(s)
- Dai Fei Elmer Ker
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, New Territories, Hong Kong SAR.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, New Territories, Hong Kong SAR
| | - Yunzhi Peter Yang
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA 94305, USA. .,Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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