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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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2
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Chen W, Chen H, Liao J, Tang M, Qin H, Zhao Z, Liu X, Wu Y, Jiang L, Zhang L, Fang B, Feng X, Zhang B, Reid K, Merilä J. Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation. Front Zool 2023; 20:1. [PMID: 36604706 PMCID: PMC9817415 DOI: 10.1186/s12983-022-00482-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. RESULTS The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. CONCLUSIONS Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.
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Affiliation(s)
- Wei Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China ,Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi, 247230 China ,grid.252245.60000 0001 0085 4987Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, 230601 China
| | - Hongzhou Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Jiahong Liao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Min Tang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Haifen Qin
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Zhenkun Zhao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Xueyan Liu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Yanfang Wu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Lichun Jiang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Lixia Zhang
- grid.462338.80000 0004 0605 6769Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Bohao Fang
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA USA
| | - Xueyun Feng
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Baowei Zhang
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China
| | - Kerry Reid
- grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland ,grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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3
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Wang F, Guo Y, Liu Z, Wang Q, Jiang Y, Zhao G. New insights into the novel sequences of the chicken pan-genome by liquid chip. J Anim Sci 2022; 100:6759641. [PMID: 36223424 PMCID: PMC9733507 DOI: 10.1093/jas/skac336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/11/2022] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence indicates that the missing sequences and genes in the chicken reference genome are involved in many crucial biological pathways, including metabolism and immunity. The low detection rate of novel sequences by resequencing hindered the acquisition of these sequences and the exploration of the relationship between new genes and economic traits. To improve the capture ratio of novel sequences, a 48K liquid chip including 25K from the reference sequence and 23K from the novel sequence was designed. The assay was tested on a panel of 218 animals from 5 chicken breeds. The average capture ratio of the reference sequence was 99.55%, and the average sequencing depth of the target sites was approximately 187X, indicating a good performance and successful application of liquid chips in farm animals. For the target region in the novel sequence, the average capture ratio was 33.15% and the average sequencing depth of target sites was approximately 60X, both of which were higher than that of resequencing. However, the different capture ratios and capture regions among varieties and individuals proved the difficulty of capturing these regions with complex structures. After genotyping, GWAS showed variations in novel sequences potentially relevant to immune-related traits. For example, a SNP close to the differentiation of lymphocyte-related gene IGHV3-23-like was associated with the H/L ratio. These results suggest that targeted capture sequencing is a preferred method to capture these sequences with complex structures and genes potentially associated with immune-related traits.
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Affiliation(s)
| | | | | | - Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 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, Shaanxi, China
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Sharma A, Gupta S, Patil AB, Vijay N. Birth and death in terminal complement pathway. Mol Immunol 2022; 149:174-187. [PMID: 35908437 DOI: 10.1016/j.molimm.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 10/16/2022]
Abstract
The cytolytic activity of the membrane attack complex (MAC) is pivotal in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrate C6 gene. The subsequent duplication and divergence of this vertebrate C6 gene formed the C7, C8α, C8β, and C9 genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered that C9 has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at the C9 locus. In this study, we have generated a > 120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of the C9 gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons of C9 in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred after C9 gene loss in an early galliform ancestor. Loss of C9 in galliform birds, in contrast to conservation in other vertebrates, may have implications for host-pathogen interactions. Our study of C6 gene birth in an early vertebrate ancestor and C9 gene death in galliform birds provides insights into the evolution of the TCP.
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Affiliation(s)
- Ashutosh Sharma
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Saumya Gupta
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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Burkhardt NB, Elleder D, Schusser B, Krchlíková V, Göbel TW, Härtle S, Kaspers B. The Discovery of Chicken Foxp3 Demands Redefinition of Avian Regulatory T Cells. J Immunol 2022; 208:1128-1138. [PMID: 35173035 DOI: 10.4049/jimmunol.2000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 12/17/2021] [Indexed: 11/19/2022]
Abstract
Since the publication of the first chicken genome sequence, we have encountered genes playing key roles in mammalian immunology, but being seemingly absent in birds. One of those was, until recently, Foxp3, the master transcription factor of regulatory T cells in mammals. Therefore, avian regulatory T cell research is still poorly standardized. In this study we identify a chicken ortholog of Foxp3 We prove sequence homology with known mammalian and sauropsid sequences, but also reveal differences in major domains. Expression profiling shows an association of Foxp3 and CD25 expression levels in CD4+CD25+ peripheral T cells and identifies a CD4-CD25+Foxp3high subset of thymic lymphocytes that likely represents yet undescribed avian regulatory T precursor cells. We conclude that Foxp3 is existent in chickens and that it shares certain functional characteristics with its mammalian ortholog. Nevertheless, pathways for regulatory T cell development and Foxp3 function are likely to differ between mammals and birds. The identification and characterization of chicken Foxp3 will help to define avian regulatory T cells and to analyze their functional properties and thereby advance the field of avian immunology.
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Affiliation(s)
- Nina B Burkhardt
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Daniel Elleder
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic; and
| | - Benjamin Schusser
- Reproductive Biotechnology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Veronika Krchlíková
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic; and
| | - Thomas W Göbel
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Sonja Härtle
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Bernd Kaspers
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany;
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Kato M, Iwakoshi-Ukena E, Furumitsu M, Ukena K. A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks. Front Physiol 2021; 12:747473. [PMID: 34759838 PMCID: PMC8573243 DOI: 10.3389/fphys.2021.747473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 12/25/2022] Open
Abstract
We recently discovered a novel cDNA encoding the precursor of a small secretory protein, neurosecretory protein GM (NPGM), in the mediobasal hypothalamus of chickens. Although our previous study showed that subcutaneous infusion of NPGM for 6 days increased body mass in chicks, the chronic effect of intracerebroventricular (i.c.v.) infusion of NPGM remains unknown. In this study, we performed i.c.v. administration of NPGM in eight-day-old layer chicks using osmotic pumps for 2 weeks. In the results, chronic i.c.v. infusion of NPGM significantly increased body mass, water intake, and the mass of abdominal and gizzard fat in chicks, whereas NPGM did not affect food intake, liver and muscle masses, or blood glucose concentration. Morphological analyses using Oil Red O and hematoxylin-eosin stainings revealed that fat accumulation occurred in both the liver and gizzard fat after NPGM infusion. The real-time PCR analysis showed that NPGM decreased the mRNA expression of peroxisome proliferator-activated receptor α, a lipolytic factor in the liver. These results indicate that NPGM may participate in fat storage in chicks.
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Affiliation(s)
- Masaki Kato
- Laboratory of Neurometabolism, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Eiko Iwakoshi-Ukena
- Laboratory of Neurometabolism, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Megumi Furumitsu
- Laboratory of Neurometabolism, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kazuyoshi Ukena
- Laboratory of Neurometabolism, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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Sharma V, Young B, Armogida L, Khan A, Wurmbach E. Evaluation of ArmedXpert software tools, MixtureAce and Mixture Interpretation, to analyze MPS-STR data. Forensic Sci Int Genet 2021; 56:102603. [PMID: 34673336 DOI: 10.1016/j.fsigen.2021.102603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022]
Abstract
Massively parallel sequencing (MPS) technologies have revolutionized studies of genomic variations and transformed DNA analysis in multiple fields. Assays based on MPS must be capable of discriminating variations introduced by the method, i.e. artifacts from true polymorphisms. In PCR-MPS methods targeting microsatellite markers, artifacts can arise from PCR mis-incorporation, PCR strand slippage (stutter), and sequencing error. Reliable detection of artifacts in mixed DNA samples is a significant challenge that must be addressed in forensic DNA analysis. The ArmedXpert (NicheVision) software tools, MixtureAce™ and Mixture Interpretation, can analyze MPS data by categorizing sequence reads in alleles, stutter, and non-stutter artifacts and analyzing autosomal STR loci of mixed samples. In this study, we evaluated the ArmedXpert tools for the analysis of STR profiles of single-sourced and mixed samples generated by the ForenSeq™ DNA Signature Prep kit (Verogen). Data from eight experimental runs (240 samples) were analyzed: one benchmark run, two runs testing sensitivity with down to 50 pg DNA input, one run testing artificially degraded samples and DNA derived from bones, blood cards and teeth, as well as four runs with mixed DNA samples of varying ratios, sex, and different number of contributors (two to six). The MixtureAce stutter thresholds were initially set following the recommendations from Verogen, plus a non-stutter artifact threshold was set at 5% of allele read counts. A benchmark run, of 30 samples, plus two controls, containing 2310 total alleles, revealed over 5000 artifacts, above an analytical threshold of 10. A total of 4869 artifacts were correctly classified, while 435 were mis-classified as alleles due to exceedance of initial threshold settings. False positives must be resolved by an analyst, which can be time consuming. Stutter thresholds were adjusted based on the benchmark data and the samples were re-tested, resulting in only 57 false positive allele calls. The revised settings were then used in the analysis of the remaining seven experimental runs. Results show that MixtureAce can accurately classify artifacts and alleles when laboratory-specific threshold settings are used. The Mixture Interpretation tool was applied on two- and three-person mixtures. This tool utilized the analyzed data from MixtureAce to calculate, based on the number of alleles at a locus and their read counts, possible deconvolution outcomes with their respective ratios.
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Affiliation(s)
- Vishakha Sharma
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA
| | - Brian Young
- NicheVision Forensics, LLC., 526 South Main Street, Akron, OH 44311, USA
| | - Luigi Armogida
- NicheVision Forensics, LLC., 526 South Main Street, Akron, OH 44311, USA
| | - Amber Khan
- New York City Public Health Laboratory, Department of Health and Mental Hygiene, 455 East 26th Street, New York, NY 10016, USA
| | - Elisa Wurmbach
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA.
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Bernardi O, Estienne A, Reverchon M, Bigot Y, Froment P, Dupont J. Adipokines in metabolic and reproductive functions in birds: An overview of current knowns and unknowns. Mol Cell Endocrinol 2021; 534:111370. [PMID: 34171419 DOI: 10.1016/j.mce.2021.111370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Abstract
Adipose tissue is now recognized as an active endocrine organ, which synthesizes and secretes numerous peptides factors called adipokines. In mammals, they exert pleiotropic effects affecting energy metabolism but also fertility. In mammals, secretion of adipokines is altered in adipose tissue dysfunctions and may participate to obesity-associated disorders. Thus, adipokines are promising candidates both for novel pharmacological treatment strategies and as diagnostic tools. As compared to mammals, birds exhibit several unique physiological features, which make them an interesting model for comparative studies on endocrine control of metabolism and adiposity and reproductive functions. Some adipokines such as leptin and visfatin may have different roles in avian species as compared to mammals. In addition, some of them found in mammals such as CCL2 (chemokine ligand 2), resistin, omentin and FGF21 (Fibroblast Growth factor 21) have not yet been mapped to the chicken genome model and among its annotated gene models. This brief review aims to summarize data (structure, metabolic and reproductive roles and molecular mechanisms involved) related to main avian adipokines (leptin, adiponectin, visfatin, and chemerin) and we will briefly discuss the adipokines that are still lacking in avian species.
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Affiliation(s)
- Ophélie Bernardi
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France; SYSAAF-Syndicat des Sélectionneurs Avicoles et Aquacoles Français, Centre INRA Val de Loire, F-37380, Nouzilly, France
| | - Anthony Estienne
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Maxime Reverchon
- SYSAAF-Syndicat des Sélectionneurs Avicoles et Aquacoles Français, Centre INRA Val de Loire, F-37380, Nouzilly, France
| | - Yves Bigot
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Pascal Froment
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France
| | - Joëlle Dupont
- CNRS, IFCE, INRAE, Université de Tours, PRC, F-37380, Nouzilly, France.
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Charlesworth D, Zhang Y, Bergero R, Graham C, Gardner J, Yong L. Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species. Mol Biol Evol 2021; 37:3550-3562. [PMID: 32697821 DOI: 10.1093/molbev/msaa187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and third positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localization in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localization than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of guppy chromosomes, which were not determined in the genome assembly.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yexin Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Falmouth, Cornwall, United Kingdom
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11
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Estienne A, Ramé C, Ganier P, Chahnamian M, Barbe A, Grandhaye J, Dubois JP, Batailler M, Migaud M, Lecompte F, Adriaensen H, Froment P, Dupont J. Chemerin impairs food intake and body weight in chicken: Focus on hypothalamic neuropeptides gene expression and AMPK signaling pathway. Gen Comp Endocrinol 2021; 304:113721. [PMID: 33493505 DOI: 10.1016/j.ygcen.2021.113721] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/31/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022]
Abstract
Unlike mammals, the role of adipokines and more particularly of chemerin in the regulation of food intake is totally unknown in avian species. Here we investigated the effect of chemerin on the food and water consumption and on the body weight in chicken. We studied the effects on the plasma glucose and insulin concentrations and the hypothalamic neuropeptides and AMPK signaling pathway. Female broiler chickens were intraperitoneally injected, daily for 13 days with either vehicle (saline; n = 25) or chemerin (8 μg/kg; n = 25 and 16 μg/kg; n = 25). Food and water intakes were recorded 24 h after each administration. Overnight fasted animals were sacrificed at day 13 (D13), 24 h after the last injection and hypothalamus and left cerebral hemispheres were collected. Chemerin and its receptors protein levels were determined by western-blot. Gene expression of neuropeptide Y (Npy), agouti-related peptide (Agrp), corticotrophin releasing hormone (Crh), pro-opiomelanocortin (Pomc), cocaine and amphetamine-regulated transcript (Cart) and Taste 1 Receptor Member 1 (Tas1r1) were evaluated by RT-qPCR. In chicken, we found that the protein amount of chemerin, CCRL2 and GPR1 was similar in left cerebral hemisphere and hypothalamus whereas CMKLR1 was higher in hypothalamus. Chemerin administration (8 and 16 μg/kg) decreased both food intake and body weight compared to vehicle without affecting water intake and the size or volume of different brain subdivisions as determined by magnetic resonance imaging. It also increased plasma insulin levels whereas glucose levels were decreased. These data were associated with an increase in Npy and Agrp expressions and a decrease in Crh, Tas1r1 mRNA expression within the hypothalamus. Furthermore, chemerin decreased hypothalamic CMKLR1 protein expression and AMPK activation. Taken together, these results support that chemerin could be a peripheral appetite-regulating signal through modulation of hypothalamic peptides expression in chicken.
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Affiliation(s)
- Anthony Estienne
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Christelle Ramé
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Patrice Ganier
- INRAE - Unité Expérimentale du Pôle d'Expérimentation Avicole de Tours UEPEAT, 1295, Nouzilly, France
| | - Marine Chahnamian
- INRAE - Unité Expérimentale du Pôle d'Expérimentation Avicole de Tours UEPEAT, 1295, Nouzilly, France
| | - Alix Barbe
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Jérémy Grandhaye
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Jean-Philippe Dubois
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Martine Batailler
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Martine Migaud
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - François Lecompte
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Hans Adriaensen
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Pascal Froment
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France
| | - Joëlle Dupont
- INRAE UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France CNRS UMR7247 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France Université François Rabelais de Tours F-37041 Tours, France IFCE F-37380 Nouzilly, France.
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Sharma S, Shinde SS, Teekas L, Vijay N. Evidence for the loss of plasminogen receptor KT gene in chicken. Immunogenetics 2020; 72:507-515. [PMID: 33247773 DOI: 10.1007/s00251-020-01186-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/03/2020] [Indexed: 12/31/2022]
Abstract
The loss of conserved genes has the potential to alter phenotypes drastically. Screening of vertebrate genomes for lineage-specific gene loss events has identified numerous natural knockouts associated with specific phenotypes. We provide evidence for the loss of a multi-exonic plasminogen receptor KT (PLGRKT) protein-encoding gene located on the Z chromosome in chicken. Exons 1 and 2 are entirely missing; remnants of exon 3 and a mostly intact exon 4 are identified in an assembly gap-free region in chicken with conserved synteny across species and verified using transcriptome and genome sequencing. PLGRKT gene disrupting changes are present in representative species from all five galliform families. In contrast to this, the presence of an intact transcriptionally active PLGRKT gene in species such as mallard, swan goose, and Anolis lizard suggests that gene loss occurred in the galliform lineage sometime between 68 and 80 Mya. The presence of galliform specific chicken repeat 1 (CR1) insertion at the erstwhile exon 2 of PLGRKT gene suggests repeat insertion-mediated loss. However, at least nine other independent PLGRKT coding frame disrupting changes in other bird species are supported by genome sequencing and indicate a role for relaxed purifying selection before CR1 insertion. The recurrent loss of a conserved gene with a role in the regulation of macrophage migration, efferocytosis, and blood coagulation is intriguing. Hence, we propose potential candidate genes that might be compensating the function of PLGRKT based on the presence of a C-terminal lysine residue, transmembrane domains, and gene expression patterns.
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Affiliation(s)
- Sandhya Sharma
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Sagar Sharad Shinde
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Lokdeep Teekas
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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