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Estay-Ahumada CE, Verra DM, Roux M, Sassone F, Felder-Schmittbuhl MP, Klopp C, Ciocca D, Moal MLL, Hicks D. Hyperglycemia and circadian disruption lead to retinal dysfunction in a stabilized colony of the fat sand rat Psammomys obesus. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167118. [PMID: 38490291 DOI: 10.1016/j.bbadis.2024.167118] [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: 10/30/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
PURPOSE The Fat Sand Rat (Psammomys obesus) recapitulates several features of human pre-proliferative diabetic retinopathy, but data are restricted to wild animals, incompatible with stringent biomedical research criteria. To overcome this barrier, we characterized retinal changes in a colony of P. obsesus maintained under strictly controlled housing conditions. METHODS Animals were maintained on low or high caloric energy diets, and raised under either standard (12 h light/12 h dark) or shortened (5 h light/5 h dark) photoperiods. Visual responses were tested by electroretinography, while structural/molecular changes were assayed by immunochemistry and molecular biology (RNAseq and qPCR). RESULTS Whereas high calorie diet alone did not induce hyperglycemia, coupled with short photoperiod >80 % animals developed severe hyper-insulinemia by 15 weeks, and 16 % animals further developed hyperglycemia. In these groups, electroretinography showed significant declines in visual responses in both hyper-insulinemic and hyperglycemic animals, especially in photopic (cone) responses. Transcriptomics analysis of hyperglycemic compared to low caloric controls revealed major upregulation in pathways involved in glial activation, extracellular matrix remodeling, inflammation, cytokine production, partial ischemic responses and angiogenesis. Western blotting against rhodopsin and cone opsin also showed decreased levels in both groups, overall decreases being greater for cones than rods in hyperglycemic animals. CONCLUSIONS P. obesus maintained in rigorously monitored captive conditions, albeit showing attenuated responses to dietary overload compared to wild counterparts, nevertheless do develop some retinal features of diabetic retinopathy-like degeneration. Such a colony with known sanitary status opens their broader use for biomedical research.
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Affiliation(s)
- Catherine E Estay-Ahumada
- Institut des Neurosciences Cellulaires et Intégratives CNRS UPR 3212, 8 Allée du Général Rouvillois, 67000 Strasbourg, France.
| | - Daniela M Verra
- Institut des Neurosciences Cellulaires et Intégratives CNRS UPR 3212, 8 Allée du Général Rouvillois, 67000 Strasbourg, France
| | - Michel Roux
- IGBMC - CNRS UMR 7104 Inserm U 1258, 1 rue Laurent Fries, BP 10142, 67404 Illkirch CEDEX, France.
| | - Fabiana Sassone
- Institut des Neurosciences Cellulaires et Intégratives CNRS UPR 3212, 8 Allée du Général Rouvillois, 67000 Strasbourg, France.
| | - Marie-Paule Felder-Schmittbuhl
- Institut des Neurosciences Cellulaires et Intégratives CNRS UPR 3212, 8 Allée du Général Rouvillois, 67000 Strasbourg, France.
| | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, BioInfoMics, MIAT UR875, INRAE, Castanet Tolosan, France.
| | - Dominique Ciocca
- Chronobiotron CNRS UMR 3415, 8 Allée Rouvillois, 67000 Strasbourg, France.
| | - Myriam Ly-Le Moal
- Institut Roche, 4 cours de l'île Seguin, 92100 Boulogne-Billancourt, France.
| | - David Hicks
- Institut des Neurosciences Cellulaires et Intégratives CNRS UPR 3212, 8 Allée du Général Rouvillois, 67000 Strasbourg, France.
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2
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Kyriacou RG, Mulhair PO, Holland PWH. GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences. J Mol Evol 2024; 92:138-152. [PMID: 38491221 PMCID: PMC10978632 DOI: 10.1007/s00239-024-10160-5] [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: 02/06/2024] [Indexed: 03/18/2024]
Abstract
The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.
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Affiliation(s)
- Riccardo G Kyriacou
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter O Mulhair
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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3
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Leow SS, Khoo JS, Ng SM, Lee WK, Hoh CC, Fairus S, Sambanthamurthi R, Hayes KC. Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human. Genetica 2024; 152:11-29. [PMID: 38099985 DOI: 10.1007/s10709-023-00202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/05/2023] [Indexed: 03/09/2024]
Abstract
The African grass or Nile rat (NR) (Arvicanthis niloticus) is a herbivorous diurnal rodent which is used as a biological model for research on type 2 diabetes mellitus (T2DM) and the circadian rhythm. Similar to humans, male NRs develop T2DM with high-carbohydrate diets. The NR thus provides a unique opportunity to identify the nutritional and underlying genetic factors that characterise human T2DM, as well as the effects of potential anti-diabetic phytochemicals such as Water-Soluble Palm Fruit Extract. Whole genome sequencing (WGS) could help identify possible genetic causes why NRs spontaneously develop T2DM in captivity. In this study, we performed WGS on a hepatic deoxyribonucleic acid (DNA) sample isolated from a male NR using PacBio high-fidelity long-read sequencing. The WGS data obtained were then de novo assembled and annotated using PacBio HiFi isoform sequencing (Iso-Seq) data as well as previous Illumina RNA sequencing (RNA-Seq) data. Genes related to insulin and circadian rhythm pathways were present in the NR genome, similar to orthologues in the rat, mouse and human genomes. T2DM development in the NR is thus most likely not attributable to structural differences in these genes when compared to other biological models. Further studies are warranted to gain additional insights on the genetic-environmental factors which underlie the genetic permissiveness of NRs to develop T2DM.
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Affiliation(s)
- Soon-Sen Leow
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Jia-Shiun Khoo
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Siuk-Mun Ng
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Wei-Kang Lee
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Syed Fairus
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
- Academy of Sciences Malaysia, Level 20, West Wing, MATRADE Tower, Jalan Sultan Haji Ahmad Shah, Off Jalan Tuanku Abdul Halim, 50480, Kuala Lumpur, Malaysia
| | - K C Hayes
- Brandeis University, 415 South Street, Waltham, MA, 02454, USA
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Courcelle M, Fabre PH, Douzery EJP. Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents. Genome Biol Evol 2023; 15:evad197. [PMID: 37972291 PMCID: PMC10653590 DOI: 10.1093/gbe/evad197] [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] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.
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Affiliation(s)
- Maxime Courcelle
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- CIRAD, UMR ASTRE, Montpellier, France
| | - Pierre-Henri Fabre
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, United Kingdom
- Institut Universitaire de France (IUF), Section Biologie-Médecine-Santé, Paris, France
| | - Emmanuel J P Douzery
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation. Sci Rep 2021; 11:24437. [PMID: 34952909 PMCID: PMC8709867 DOI: 10.1038/s41598-021-04077-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.
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Rocha JL, Godinho R, Brito JC, Nielsen R. Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation. Trends Ecol Evol 2021; 36:637-650. [PMID: 33863602 DOI: 10.1016/j.tree.2021.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.
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Affiliation(s)
- Joana L Rocha
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa
| | - José C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA; Globe Institute, University of Copenhagen, DK-1165 Copenhagen, Denmark.
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Compromised Function of the Pancreatic Transcription Factor PDX1 in a Lineage of Desert Rodents. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09544-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractGerbils are a subfamily of rodents living in arid regions of Asia and Africa. Recent studies have shown that several gerbil species have unusual amino acid changes in the PDX1 protein, a homeodomain transcription factor essential for pancreatic development and β-cell function. These changes were linked to strong GC-bias in the genome that may be caused by GC-biased gene conversion, and it has been hypothesized that this caused accumulation of deleterious changes. Here we use two approaches to examine if the unusual changes are adaptive or deleterious. First, we compare PDX1 protein sequences between 38 rodents to test for association with habitat. We show the PDX1 homeodomain is almost totally conserved in rodents, apart from gerbils, regardless of habitat. Second, we use ectopic gene overexpression and gene editing in cell culture to compare functional properties of PDX1 proteins. We show that the divergent gerbil PDX1 protein inefficiently binds an insulin gene promoter and ineffectively regulates insulin expression in response to high glucose in rat cells. The protein has, however, retained the ability to regulate some other β-cell genes. We suggest that during the evolution of gerbils, the selection-blind process of biased gene conversion pushed fixation of mutations adversely affecting function of a normally conserved homeodomain protein. We argue these changes were not entirely adaptive and may be associated with metabolic disorders in gerbil species on high carbohydrate diets. This unusual pattern of molecular evolution could have had a constraining effect on habitat and diet choice in the gerbil lineage.
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Abstract
Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
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Affiliation(s)
- Rodrigo Pracana
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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Dai Y, Pracana R, Holland PWH. Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance. BMC Evol Biol 2020; 20:134. [PMID: 33076817 PMCID: PMC7574485 DOI: 10.1186/s12862-020-01696-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Two gerbil species, sand rat (Psammomys obesus) and Mongolian jird (Meriones unguiculatus), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic basis of this phenotype is unknown. Recently, genome sequencing has uncovered very unusual regions of high guanine and cytosine (GC) content scattered across the sand rat genome, most likely generated by extreme and localized biased gene conversion. A key pancreatic transcription factor PDX1 is encoded by a gene in the most extreme GC-rich region, is remarkably divergent and exhibits altered biochemical properties. Here, we ask if gerbils have proteins in addition to PDX1 that are aberrantly divergent in amino acid sequence, whether they have also become divergent due to GC-biased nucleotide changes, and whether these proteins could plausibly be connected to metabolic dysfunction exhibited by gerbils. Results We analyzed ~ 10,000 proteins with 1-to-1 orthologues in human and rodents and identified 50 proteins that accumulated unusually high levels of amino acid change in the sand rat and 41 in Mongolian jird. We show that more than half of the aberrantly divergent proteins are associated with GC biased nucleotide change and many are in previously defined high GC regions. We highlight four aberrantly divergent gerbil proteins, PDX1, INSR, MEDAG and SPP1, that may plausibly be associated with dietary metabolism. Conclusions We show that through the course of gerbil evolution, many aberrantly divergent proteins have accumulated in the gerbil lineage, and GC-biased nucleotide substitution rather than positive selection is the likely cause of extreme divergence in more than half of these. Some proteins carry putatively deleterious changes that could be associated with metabolic and physiological phenotypes observed in some gerbil species. We propose that these animals provide a useful model to study the ‘tug-of-war’ between natural selection and the excessive accumulation of deleterious substitutions mutations through biased gene conversion.
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Affiliation(s)
- Yichen Dai
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Rodrigo Pracana
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Wang Y, Zhao P, Song Z, Du X, Huo X, Lu J, Liu X, Lv J, Li C, Guo M, Chen Z. Generation of Gene-Knockout Mongolian Gerbils via CRISPR/Cas9 System. Front Bioeng Biotechnol 2020; 8:780. [PMID: 32733872 PMCID: PMC7360674 DOI: 10.3389/fbioe.2020.00780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/18/2020] [Indexed: 12/27/2022] Open
Abstract
The Mongolian gerbil (Meriones unguiculatus), a well-known "multifunctional" experimental animal, plays a crucial role in the research of hearing, cerebrovascular diseases and Helicobacter pylori infection. Although the whole-genome sequencing of Mongolian gerbils has been recently completed, lack of valid gene-editing systems for gerbils largely limited the further usage of Mongolian gerbils in biomedical research. Here, efficient targeted mutagenesis in Mongolian gerbils was successfully conducted by pronuclear injection with Cas9 protein and single-guide RNAs (sgRNAs) targeting Cystatin C (Cst3) or Apolipoprotein A-II (Apoa2). We found that 22 h after human chorionic gonadotropin (hCG) injection, zygote microinjection was conducted, and the injected zygotes were transferred into the pseudopregnant gerbils, which were induced by injecting equine chorionic gonadotropin (eCG) and hCG at a 70 h interval and being caged with ligated male gerbils. We successfully obtained Cst3 and Apoa2 gene knockout gerbils with the knockout efficiencies of 55 and 30.9%, respectively. No off-target effects were detected in all knockout gerbils and the mutations can be germline-transmitted. The absence of CST3 protein was observed in the tissues of homozygous Cst3 knockout (Cst3-KO) gerbils. Interestingly, we found that disruption of the Cst3 gene led to more severe brain damage and neurological deficits after unilateral carotid artery ligation, thereby indicating that the gene modifications happened at both genetic and functional levels. In conclusion, we successfully generated a CRISPR/Cas9 system based genome editing platform for Mongolian gerbils, which provided a foundation for obtaining other genetically modified gerbil models for biomedical research.
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Affiliation(s)
- Yan Wang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Peikun Zhao
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Zidai Song
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Xiaoyan Du
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Xueyun Huo
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Jing Lu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Xin Liu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Jianyi Lv
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Changlong Li
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Meng Guo
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Zhenwen Chen
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, School of Basic Medical Science, Capital Medical University, Beijing, China
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Sahraoui A, Dewachter C, Vegh G, Mc Entee K, Naeije R, Bouguerra SA, Dewachter L. High fat diet altered cardiac metabolic gene profile in Psammomys obesus gerbils. Lipids Health Dis 2020; 19:123. [PMID: 32493392 PMCID: PMC7271448 DOI: 10.1186/s12944-020-01301-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 05/22/2020] [Indexed: 01/18/2023] Open
Abstract
Background In metabolic disorders, myocardial fatty infiltration is critically associated with lipotoxic cardiomyopathy. Methods Twenty Psammomys obesus gerbils were randomly assigned to normal plant or high fat diet. Sixteen weeks later, myocardium was sampled for pathobiological evaluation. Results A sixteen-week high fat diet resulted in myocardial structure disorganization, with collagen deposits, lipid accumulation, cardiomyocyte apoptosis and inflammatory cell infiltration. Myocardial expressions of glucose transporter GLUT1 and pyruvate dehydrogenase (PDH) inhibitor, PDH kinase (PDK)4 increased, while insulin-regulated GLUT4 expression remained unchanged. Myocardial expressions of molecules regulating fatty acid transport, CD36 and fatty acid binding protein (FABP)3, were increased, while expression of rate-controlling fatty acid β-oxidation, carnitine palmitoyl transferase (CPT)1B decreased. Myocardial expression of AMP-activated protein kinase (AMPK), decreased, while expression of peroxisome proliferator activated receptors (PPAR)-α and -γ did not change. Conclusion In high fat diet fed Psammomys obesus, an original experimental model of nutritionally induced metabolic syndrome mixing genetic predisposition and environment interactions, a short period of high fat feeding was sufficient to induce myocardial structural alterations, associated with altered myocardial metabolic gene expression in favor of lipid accumulation.
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Affiliation(s)
- Abdelhamid Sahraoui
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium.,Team of Cellular and Molecular Physiopathology, Faculty of Biological Sciences, Houari Boumediene University of Sciences and Technology, El Alia, Algiers, Algeria.,Faculté des Sciences de la Nature et de la Vie & des Sciences de la Terre, University Djilali Bounaama of Khemis Miliana, 44225, Khemis Miliana, Algeria
| | - Céline Dewachter
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium.,Department of Cardiology, Cliniques Universitaires de Bruxelles, Hôpital Académique Erasme, Bruxelles, Belgium
| | - Grégory Vegh
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium
| | - Kathleen Mc Entee
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium
| | - Robert Naeije
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium
| | - Souhila Aouichat Bouguerra
- Team of Cellular and Molecular Physiopathology, Faculty of Biological Sciences, Houari Boumediene University of Sciences and Technology, El Alia, Algiers, Algeria
| | - Laurence Dewachter
- Laboratory of Physiology and Pharmacology, Faculty of Medicine, Université Libre de Bruxelles, 808, Lennik Road, 1070, Brussels, Belgium.
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12
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Nilsson P, Solbakken MH, Schmid BV, Orr RJS, Lv R, Cui Y, Song Y, Zhang Y, Baalsrud HT, Tørresen OK, Stenseth NC, Yang R, Jakobsen KS, Easterday WR, Jentoft S. The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biol Evol 2020; 12:3832-3849. [PMID: 31971556 PMCID: PMC7046166 DOI: 10.1093/gbe/evaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | | | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujiang Zhang
- Xinjiang Center for Disease Control and Prevention, Urumqi, China
| | - Helle T Baalsrud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - William Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
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13
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Dai Y, Holland PWH. The Interaction of Natural Selection and GC Skew May Drive the Fast Evolution of a Sand Rat Homeobox Gene. Mol Biol Evol 2020; 36:1473-1480. [PMID: 30968125 PMCID: PMC6573468 DOI: 10.1093/molbev/msz080] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Several processes can lead to strong GC skew in localized genomic regions. In most cases, GC skew should not affect conserved amino acids because natural selection will purge deleterious alleles. However, in the gerbil subfamily of rodents, several conserved genes have undergone radical alteration in association with strong GC skew. An extreme example concerns the highly conserved homeobox gene Pdx1, which is uniquely divergent and GC rich in the sand rat Psammomys obesus and close relatives. Here, we investigate the antagonistic interplay between very rare amino acid changes driven by GC skew and the force of natural selection. Using ectopic protein expression in cell culture, pulse-chase labeling, in vitro mutagenesis, and drug treatment, we compare properties of mouse and sand rat Pdx1 proteins. We find that amino acid change driven by GC skew resulted in altered protein stability, with a significantly longer protein half-life for sand rat Pdx1. Using a reversible inhibitor of the 26S proteasome, MG132, we find that sand rat and mouse Pdx1 are both degraded through the ubiquitin proteasome pathway. However, in vitro mutagenesis reveals this pathway operates through different amino acid residues. We propose that GC skew caused loss of a key ubiquitination site, conserved through vertebrate evolution, and that sand rat Pdx1 evolved or fixed a new ubiquitination site to compensate. Our results give molecular insight into the power of natural selection in the face of maladaptive changes driven by strong GC skew.
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Affiliation(s)
- Yichen Dai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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14
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Verra DM, Sajdak BS, Merriman DK, Hicks D. Diurnal rodents as pertinent animal models of human retinal physiology and pathology. Prog Retin Eye Res 2019; 74:100776. [PMID: 31499165 DOI: 10.1016/j.preteyeres.2019.100776] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022]
Abstract
This presentation will survey the retinal architecture, advantages, and limitations of several lesser-known rodent species that provide a useful diurnal complement to rats and mice. These diurnal rodents also possess unusually cone-rich photoreceptor mosaics that facilitate the study of cone cells and pathways. Species to be presented include principally the Sudanian Unstriped Grass Rat and Nile Rat (Arvicanthis spp.), the Fat Sand Rat (Psammomys obesus), the degu (Octodon degus) and the 13-lined ground squirrel (Ictidomys tridecemlineatus). The retina and optic nerve in several of these species demonstrate unusual resilience in the face of neuronal injury, itself an interesting phenomenon with potential translational value.
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Affiliation(s)
- Daniela M Verra
- Department of Neurobiology of Rhythms, Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS UPR 3212, Strasbourg, France
| | | | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - David Hicks
- Department of Neurobiology of Rhythms, Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS UPR 3212, Strasbourg, France.
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15
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Pluripotent stem cell-derived organogenesis in the rat model system. Transgenic Res 2019; 28:287-297. [PMID: 31254209 DOI: 10.1007/s11248-019-00161-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/26/2019] [Indexed: 12/21/2022]
Abstract
Rats make an excellent model system for studying xenotransplantation since, like mice pluripotent stem cell lines, such as embryonic stem cells and induced pluripotent stem cells as well as gene knock-outs are also available for rats, besides rats have larger organs. The emergence of new genome-editing tools combined with stem cell technology, has revolutionized biomedical research including the field of regenerative medicine. The aim of this manuscript is to provide an overview of the recent progresses in stem cell-derived organ regeneration involving "gene knock-out" and "blastocyst complementation" in the rat model system. Knocking-out Pdx1, Foxn1, and Sall1 genes have successfully generated rat models lacking the pancreas, thymus, and kidney, respectively. When allogeneic (rat) or xenogeneic (mouse) pluripotent stem cells were microinjected into blastocyst-stage rat embryos that had been designed to carry a suitable organogenetic niche, devoid of specific organs, the complemented blastocysts were able to develop to full-term chimeric rat offspring containing stem cell-derived functional organs in their respective niches. Thus, organs with a tridimensional structure can be generated with pluripotent stem cells in vivo, accelerating regenerative medical research, which is crucial for organ-based transplantation therapies. However, to address ethical concerns, public consent after informed discussions is essential before production of human organs within domestic animals.
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16
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Warthi G, Seligmann H. Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. PLoS One 2019; 14:e0217356. [PMID: 31120958 PMCID: PMC6532905 DOI: 10.1371/journal.pone.0217356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/09/2019] [Indexed: 11/22/2022] Open
Abstract
Raw transcriptomic data contain numerous RNA reads whose homology with template DNA doesn't match canonical transcription. Transcriptome analyses usually ignore such noncanonical RNA reads. Here, analyses search for noncanonical mitochondrial RNAs systematically deleting 1 to 12 nucleotides after each transcribed nucleotide triplet, producing deletion-RNAs (delRNAs). We detected delRNAs in the human whole cell and purified mitochondrial transcriptomes, and in Genbank's human EST database corresponding to systematic deletions of 1 to 12 nucleotides after each transcribed trinucleotide. DelRNAs detected in both transcriptomes mapped along with 55.63% of the EST delRNAs. A bias exists for delRNAs covering identical mitogenomic regions in both transcriptomic and EST datasets. Among 227 delRNAs detected in these 3 datasets, 81.1% and 8.4% of delRNAs were mapped on mitochondrial coding and hypervariable region 2 of dloop. Del-transcription analyses of GenBank's EST database confirm observations from whole cell and purified mitochondrial transcriptomes, eliminating the possibility that detected delRNAs are false positives matches, cytosolic DNA/RNA nuclear contamination or sequencing artefacts. These detected delRNAs are enriched in frameshift-inducing homopolymers and are poor in frameshift-preventing circular code codons (a set of 20 codons which regulate reading frame detection, over- and underrepresented in coding and other frames of genes, respectively) suggesting a motif-based regulation of non-canonical transcription. These findings show that rare non-canonical transcripts exist. Such non canonical del-transcription does increases mitochondrial coding potential and non-coding regulation of intracellular mechanisms, and could explain the dark DNA conundrum.
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Affiliation(s)
- Ganesh Warthi
- Aix-Marseille Université, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, IRD, MEPHI, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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17
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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18
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Laumer CE. Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices. Integr Comp Biol 2019; 58:623-639. [PMID: 29982611 DOI: 10.1093/icb/icy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
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Affiliation(s)
- Christopher E Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK
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19
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Brekke TD, Supriya S, Denver MG, Thom A, Steele KA, Mulley JF. A high-density genetic map and molecular sex-typing assay for gerbils. Mamm Genome 2019; 30:63-70. [PMID: 30972478 PMCID: PMC6491409 DOI: 10.1007/s00335-019-09799-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
We constructed a high-density genetic map for Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus: 10047.
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Affiliation(s)
- Thomas D Brekke
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Sushmita Supriya
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Megan G Denver
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Angharad Thom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Katherine A Steele
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK.
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20
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Xie KT, Wang G, Thompson AC, Wucherpfennig JI, Reimchen TE, MacColl ADC, Schluter D, Bell MA, Vasquez KM, Kingsley DM. DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science 2019; 363:81-84. [PMID: 30606845 DOI: 10.1126/science.aan1425] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/18/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023]
Abstract
Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.
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Affiliation(s)
- Kathleen T Xie
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Abbey C Thompson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Michael A Bell
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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21
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Subramaniam A, Landstrom M, Luu A, Hayes KC. The Nile Rat (Arvicanthis niloticus) as a Superior Carbohydrate-Sensitive Model for Type 2 Diabetes Mellitus (T2DM). Nutrients 2018; 10:nu10020235. [PMID: 29463026 PMCID: PMC5852811 DOI: 10.3390/nu10020235] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
Abstract
Type II diabetes mellitus (T2DM) is a multifactorial disease involving complex genetic and environmental interactions. No single animal model has so far mirrored all the characteristics or complications of diabetes in humans. Since this disease represents a chronic nutritional insult based on a diet bearing a high glycemic load, the ideal model should recapitulate the underlying dietary issues. Most rodent models have three shortcomings: (1) they are genetically or chemically modified to produce diabetes; (2) unlike humans, most require high-fat feeding; (3) and they take too long to develop diabetes. By contrast, Nile rats develop diabetes rapidly (8-10 weeks) with high-carbohydrate (hiCHO) diets, similar to humans, and are protected by high fat (with low glycemic load) intake. This review describes diabetes progression in the Nile rat, including various aspects of breeding, feeding, and handling for best experimental outcomes. The diabetes is characterized by a striking genetic permissiveness influencing hyperphagia and hyperinsulinemia; random blood glucose is the best index of disease progression; and kidney failure with chronic morbidity and death are outcomes, all of which mimic uncontrolled T2DM in humans. Non-alcoholic fatty liver disease (NAFLD), also described in diabetic humans, results from hepatic triglyceride and cholesterol accumulation associated with rising blood glucose. Protection is afforded by low glycemic load diets rich in certain fibers or polyphenols. Accordingly, the Nile rat provides a unique opportunity to identify the nutritional factors and underlying genetic and molecular mechanisms that characterize human T2DM.
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Affiliation(s)
| | | | - Alice Luu
- Department of Biology, Brandeis University, Waltham, MA 02454, USA.
| | - K C Hayes
- Department of Biology, Brandeis University, Waltham, MA 02454, USA.
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22
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Lan Y, Liu M, Cao Y. The complete mitochondrial genome of Psammomys obesus (Rodentia: Muridae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:97-98. [PMID: 33474080 PMCID: PMC7800552 DOI: 10.1080/23802359.2017.1422396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The fat sand rats (Psammomys obesus) can easily induce obesity and acquire type 2 diabetes mellitus when they are fed with high-carbohydrate diets. P. obesus is often used as an animal model for studies on diabetes and obesity. We described 16,592 bp of P. obesus mtDNA that contains 13 protein-coding genes (PGCs), two rRNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one control region (D-loop). The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of P. obesus.
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Affiliation(s)
- Yanhong Lan
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, China
| | - Mengjia Liu
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, China
| | - Yi Cao
- Microbiology and Metabolic Engineering of Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, China
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23
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Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds. Mol Biol Evol 2017; 34:3123-3131. [DOI: 10.1093/molbev/msx236] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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