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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
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Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
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3
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Verry AJF, Mas-Carrió E, Gibb GC, Dutoit L, Robertson BC, Waters JM, Rawlence NJ. Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Mol Ecol 2024; 33:e17227. [PMID: 38018770 DOI: 10.1111/mec.17227] [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: 08/02/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.
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Affiliation(s)
- Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eduard Mas-Carrió
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Gillian C Gibb
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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Chen WK, Zhang HJ, Liu J, Dai Z, Zhan XL. COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes. Int Immunopharmacol 2024; 127:111416. [PMID: 38145599 DOI: 10.1016/j.intimp.2023.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/02/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Synovial chondromatosis (SC) primarily affects the major joints and is characterized by the formation of benign cartilaginous nodules. In the present study, we evaluated the differences in the histology and gene expression of SC and normal cartilages and further elucidated the function of hub genes in SC. METHODS Histological staining and biochemical analysis were performed to measure collagen and glycosaminoglycan (GAG) contents in SC and normal cartilage samples. Then, microarray analysis was performed using knee joint samples (three normal and three SC samples) to identify the differentially expressed genes (DEGs). Subsequently, bioinformatics analysis was performed to identify the hub genes and explore the mechanisms underlying SC. The intersection of the top 10 upregulated DEGs, top 10 downregulated DEGs, and hub genes was validated in SC tissues. Lastly, in vitro experiments and our clinical cohort were used to determine the potential biological functions and diagnostic value, respectively, of the most significant gene. RESULTS The GAG and collagen contents were comparable to or higher in SC tissues than in normal tissues. Microarray analysis revealed 143 upregulated and 107 downregulated DEGs in SC. Furthermore, functional enrichment analysis revealed an association between immunity and metabolism-related pathways and SC development. Among 20 hub genes, two intersection genes, namely, collagen type III alpha 1 chain (COL3A1) and HSPA8, were notably expressed in SC tissues, with COL3A1 exhibiting a more significant difference in mRNA expression. Furthermore, COL3A1 can promote chondrocyte migration and cell cycle progression. Additionally, clinical data revealed COL3A1 can be a diagnostic marker for primary SC (AUC = 0.82) and be a positive correlation with neutrophil-to-lymphocyte ratio. CONCLUSIONS These results suggest that SC tissues contained the abundant GAG and collagen. COL3A1 can affect the function of chondrocytes and be a diagnostic marker of primary SC patients. These findings provide a novel approach and a fundamental contribution for diagnosis and treatment in SC.
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Affiliation(s)
- Wen-Kang Chen
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China; The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Han-Jing Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, No. 69 ChuanShan Road, Shigu District, Hengyang, 421001, Hunan, China
| | - Jianghua Liu
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhu Dai
- The First Affiliated Hospital, Speciality of Sports Medcine in Department of Orthopaedics, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Xin-Li Zhan
- Department of Spine and Osteopathy Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 53000, China.
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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [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: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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6
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Póliska S, Fareh C, Lengyel A, Göczi L, Tőzsér J, Szatmari I. Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells. Front Genet 2024; 14:1275383. [PMID: 38250572 PMCID: PMC10796612 DOI: 10.3389/fgene.2023.1275383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction: We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies. Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400. Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly overlapping RUNX3- and ZBTB46-regulated gene lists were obtained from both sequencing datasets. Moreover, we observed that the Standard and the Hot-MPS-derived RUNX3- and ZBTB46-regulated gene lists were also considerably overlapped. This transcriptome analysis also helped us to identify differently expressed genes in the presence of the transgenic RUNX3 or ZBTB46. For example, we found that Gzmb, Gzmd, Gzme, Gdf6, and Ccr7 genes were robustly upregulated upon the forced expression of Runx3; on the other hand, Gpx2, Tdpoz4, and Arg2 were induced alongside the ectopic expression of Zbtb46. Discussion: Similar gene expression profile and greatly overlapping RUNX3- and ZBTB46-regulated gene sets were detected with both DNA sequencing platforms. Our analyses demonstrate that both sequencing technologies are suitable for transcriptome profiling and target gene selection. These findings suggest that DNBSEQ G400 represents a cost-effective alternative sequencing platform for gene expression monitoring. Moreover, this analysis provides a resource for exploration of the RUNX3- and ZBTB46-dependent gene regulatory networks.
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Affiliation(s)
- Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Chahra Fareh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Adél Lengyel
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Loránd Göczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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7
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Lin AT, Hammond-Kaarremaa L, Liu HL, Stantis C, McKechnie I, Pavel M, Pavel SSM, Wyss SSÁ, Sparrow DQ, Carr K, Aninta SG, Perri A, Hartt J, Bergström A, Carmagnini A, Charlton S, Dalén L, Feuerborn TR, France CAM, Gopalakrishnan S, Grimes V, Harris A, Kavich G, Sacks BN, Sinding MHS, Skoglund P, Stanton DWG, Ostrander EA, Larson G, Armstrong CG, Frantz LAF, Hawkins MTR, Kistler L. The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge. Science 2023; 382:1303-1308. [PMID: 38096292 PMCID: PMC7615573 DOI: 10.1126/science.adi6549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
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Affiliation(s)
- Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
| | - Liz Hammond-Kaarremaa
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Vancouver Island University, Nanaimo, BC, Canada
| | - Hsiao-Lei Liu
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Chris Stantis
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
| | - Michael Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
| | - Susan sa'hLa mitSa Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
- Coast Salish Wool Weaving Center, Skokomish Nation, WA, USA
- The Evergreen State College, Olympia, WA, USA
| | | | | | | | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Angela Perri
- Department of Anthropology, Texas A&M University, College Station, TX, USA
- Chronicle Heritage, Phoenix, AZ, USA
| | - Jonathan Hartt
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sophy Charlton
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, NL, Canada
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gwénaëlle Kavich
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - David W G Stanton
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Greger Larson
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
| | - Chelsey G Armstrong
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Melissa T R Hawkins
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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8
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Hernández-Alonso G, Ramos-Madrigal J, van Grouw H, Ciucani MM, Cavill EL, Sinding MHS, Gopalakrishnan S, Pacheco G, Gilbert MTP. Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Mol Biol Evol 2023; 40:msad243. [PMID: 37950889 PMCID: PMC10667084 DOI: 10.1093/molbev/msad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023] Open
Abstract
The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
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Affiliation(s)
- Germán Hernández-Alonso
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, United Kingdom
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily Louisa Cavill
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - George Pacheco
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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9
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Liao R, Wu Y, Qin L, Jiang Z, Gou S, Zhou L, Hong Q, Li Y, Shi J, Yao Y, Lai L, Li Y, Liu P, Thiery JP, Qin D, Graf T, Liu X, Li P. BCL11B and the NuRD complex cooperatively guard T-cell fate and inhibit OPA1-mediated mitochondrial fusion in T cells. EMBO J 2023; 42:e113448. [PMID: 37737560 PMCID: PMC10620766 DOI: 10.15252/embj.2023113448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
The nucleosome remodeling and histone deacetylase (NuRD) complex physically associates with BCL11B to regulate murine T-cell development. However, the function of NuRD complex in mature T cells remains unclear. Here, we characterize the fate and metabolism of human T cells in which key subunits of the NuRD complex or BCL11B are ablated. BCL11B and the NuRD complex bind to each other and repress natural killer (NK)-cell fate in T cells. In addition, T cells upregulate the NK cell-associated receptors and transcription factors, lyse NK-cell targets, and are reprogrammed into NK-like cells (ITNKs) upon deletion of MTA2, MBD2, CHD4, or BCL11B. ITNKs increase OPA1 expression and exhibit characteristically elongated mitochondria with augmented oxidative phosphorylation (OXPHOS) activity. OPA1-mediated elevated OXPHOS enhances cellular acetyl-CoA levels, thereby promoting the reprogramming efficiency and antitumor effects of ITNKs via regulating H3K27 acetylation at specific targets. In conclusion, our findings demonstrate that the NuRD complex and BCL11B cooperatively maintain T-cell fate directly by repressing NK cell-associated transcription and indirectly through a metabolic-epigenetic axis, providing strategies to improve the reprogramming efficiency and antitumor effects of ITNKs.
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Affiliation(s)
- Rui Liao
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yi Wu
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Le Qin
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Zhiwu Jiang
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Shixue Gou
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Linfu Zhou
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Qilan Hong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
- Centre for Genomic RegulationThe Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Yao Li
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Jingxuan Shi
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yao Yao
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Liangxue Lai
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yangqiu Li
- Institute of HematologyMedical College, Jinan UniversityGuangzhouChina
| | - Pentao Liu
- School of Biomedical Sciences, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | | | - Dajiang Qin
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Thomas Graf
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
- Centre for Genomic RegulationThe Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Xingguo Liu
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & InnovationChinese Academy of SciencesHong Kong SARChina
| | - Peng Li
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & InnovationChinese Academy of SciencesHong Kong SARChina
- Department of SurgeryThe Chinese University of Hong KongHong Kong SARChina
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10
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Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IRM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023; 40:msad180. [PMID: 37561011 PMCID: PMC10500089 DOI: 10.1093/molbev/msad180] [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: 09/16/2022] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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Affiliation(s)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Xin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | | | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
- BGI Research, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
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11
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Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
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Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
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12
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Hernández‐Alonso G, Ramos‐Madrigal J, Sun X, Scharff‐Olsen CH, Sinding MS, Martins NF, Ciucani MM, Mak SST, Lanigan LT, Clausen CG, Bhak J, Jeon S, Kim C, Eo KY, Cho S, Boldgiv B, Gantulga G, Unudbayasgalan Z, Kosintsev PA, Stenøien HK, Gilbert MTP, Gopalakrishnan S. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecol Evol 2023; 13:e10404. [PMID: 37546572 PMCID: PMC10401669 DOI: 10.1002/ece3.10404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.
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Affiliation(s)
- Germán Hernández‐Alonso
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jazmín Ramos‐Madrigal
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Xin Sun
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Nuno F. Martins
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Sarah S. T. Mak
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Liam Thomas Lanigan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Cecilie G. Clausen
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jong Bhak
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
- Department of Biomedical Engineering, College of Information‐Bio Convergence EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
- Personal Genomics InstituteGenome Research FoundationOsongKorea
| | - Sungwon Jeon
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
| | | | - Kyung Yeon Eo
- Department of Animal Health & WelfareSemyung UniversityJecheonKorea
| | - Seong‐Ho Cho
- Natural History MuseumKyungpook National UniversityGunwiKorea
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary SynthesisNational University of MongoliaUlaanbaatarMongolia
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of SciencesYekaterinburgRussia
- Ural Federal UniversityEkaterinburgRussia
| | - Hans K. Stenøien
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - M. Thomas P. Gilbert
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Bioinformatics, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
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13
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Bazukyan I, Georgieva-Miteva D, Velikova T, Dimov SG. In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut. INSECTS 2023; 14:540. [PMID: 37367356 DOI: 10.3390/insects14060540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
A Lactobacillus delbrueckii ssp. lactis strain named A4, isolated from the gut of an Armenian honeybee, was subjected to a probiogenomic characterization because of its unusual origin. A whole-genome sequencing was performed, and the bioinformatic analysis of its genome revealed a reduction in the genome size and the number of the genes-a process typical for the adaptation to endosymbiotic conditions. Further analysis of the genome revealed that Lactobacillus delbrueckii ssp. lactis strain named A4 could play the role of a probiotic endosymbiont because of the presence of intact genetic sequences determining antioxidant properties, exopolysaccharides synthesis, adhesion properties, and biofilm formation, as well as an antagonistic activity against some pathogens which is not due to pH or bacteriocins production. Additionally, the genomic analysis revealed significant potential for stress tolerance, such as extreme pH, osmotic stress, and high temperature. To our knowledge, this is the first report of a potentially endosymbiotic Lactobacillus delbrueckii ssp. lactis strain adapted to and playing beneficial roles for its host.
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Affiliation(s)
- Inga Bazukyan
- Faculty of Biology, Yerevan State University, Yerevan 0025, Armenia
| | | | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1 Kozyak Str., 1407 Sofia, Bulgaria
| | - Svetoslav G Dimov
- Faculty of Biology, Sofia University St. Kliment Ohridski, 8 Dragan Tzankov Str., 1164 Sofia, Bulgaria
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14
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Wang Y, Yang L, Zhou H, Zhang K, Zhao M. Identification of miRNA-mediated gene regulatory networks in L-methionine exposure counteracts cocaine-conditioned place preference in mice. Front Genet 2023; 13:1076156. [PMID: 36744178 PMCID: PMC9893020 DOI: 10.3389/fgene.2022.1076156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023] Open
Abstract
Background and Aims: Methionine has been proven to inhibit addictive behaviors of cocaine dependence. This study aimed to identify the potential mechanisms of MET relating to its inhibitory effects on cocaine induced cellular and behavioral changes. Methods: MRNA and miRNA high-throughput sequencing of the prefrontal cortex in a mouse model of cocaine conditioned place preference (CPP) combined with L-methionine was performed. Differentially expressed miRNAs (DE-miRNAs) and differentially expressed genes (DEGs) regulated by cocaine and inhibited by L-methionine were identified. DEGs were mapped to STRING database to construct a protein-protein interaction (PPI) network. Then, the identified DEGs were subjected to the DAVID webserver for functional annotation. Finally, miRNA-mRNA regulatory network and miRNA-mRNA-TF regulatory networks were established to screen key DE-miRNAs and coregulation network in Cytoscape. Results: Sequencing data analysis showed that L-methionine reversely regulated genes and miRNAs affected by cocaine. Pathways associated with drug addiction only enriched in CS-down with MC-up genes targeted by DE-miRNAs including GABAergic synapse, Glutamatergic synapse, Circadian entrainment, Axon guidance and Calcium signaling pathway. Drug addiction associated network was formed of 22 DEGs including calcium channel (Cacna1c, Cacna1e, Cacna1g and Cacng8), ephrin receptor genes (Ephb6 and Epha8) and ryanodine receptor genes (Ryr1 and Ryr2). Calcium channel gene network were identified as a core gene network modulated by L-methionine in response to cocaine dependence. Moreover, it was predicted that Grin1 and Fosb presented in TF-miRNA-mRNA coregulation network with a high degree of interaction as hub genes and interacted calcium channels. Conclusion: These identified key genes, miRNA and coregulation network demonstrated the efficacy of L-methionine in counteracting the effects of cocaine CPP. To a certain degree, it may provide some hints to better understand the underlying mechanism on L-methionine in response to cocaine abuse.
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Affiliation(s)
- Yan Wang
- CAS Key Lab of Mental Health, Institute of Psychology, Beijing, China,Department of psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Lvyu Yang
- CAS Key Lab of Mental Health, Institute of Psychology, Beijing, China,Department of psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Hansheng Zhou
- Department of Pharmacy, Linyi People’s Hospital, Linyi, Shandong Province, China
| | - Kunlin Zhang
- CAS Key Lab of Mental Health, Institute of Psychology, Beijing, China
| | - Mei Zhao
- CAS Key Lab of Mental Health, Institute of Psychology, Beijing, China,Department of psychology, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Mei Zhao,
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15
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Benz S, Mitra S. From Genomics to Metagenomics in the Era of Recent Sequencing Technologies. Methods Mol Biol 2023; 2649:1-20. [PMID: 37258855 DOI: 10.1007/978-1-0716-3072-3_1] [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] [Indexed: 06/02/2023]
Abstract
Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.
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Affiliation(s)
- Saskia Benz
- School of medicine, University of Leeds, Leeds, UK
| | - Suparna Mitra
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK.
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16
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Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines. Genes (Basel) 2022; 14:genes14010075. [PMID: 36672816 PMCID: PMC9858670 DOI: 10.3390/genes14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.
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17
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Xian L, Sahu SK, Huang L, Fan Y, Lin J, Su J, Bai M, Chen Y, Wang S, Ye P, Wang F, Luo Q, Bai H, Lin X, Yuan C, Geng X, Liu H, Wu H. The draft genome and multi-omics analyses reveal new insights into geo-herbalism properties of Citrus grandis 'Tomentosa'. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111489. [PMID: 36216298 DOI: 10.1016/j.plantsci.2022.111489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Citrus grandis 'Tomentosa' (CGT) (Huajuhong, HJH) is a widely used medicinal plant, which is mainly produced in Guangdong and Guangxi provinces of South China. Particularly, HJH from Huazhou (HZ) county of Guangdong province has been well-regarded as the best national product for geo-herbalism. But the reasons for geo-herbalism property in HJH from HZ county remains a mystery. Therefore, a multi-omics approach was applied to identify the nature of the geo-herbalism in CGT from three different regions. The comprehensive screening of differential metabolites revealed that the Nobiletin content was significantly different in HZ region compared to other regions, and could be employed as a key indicator to determine the geo-herbalism. Furthermore, the high-quality genome (N50 of 9.12 Mb), coupled with genomics and transcriptomics analyses indicated that CGT and Citrus grandis are closely related, with a predicted divergence time of 19.1 million years ago (MYA), and no recent WGD occurred in the CGT, and the bioactive ingredients of CGT were more abundant than that of Citrus grandis. Interestingly, Nobiletin (Polymethoxyflavones) content was identified as a potential indicator of geo-herbalism, and O-methyltransferase (OMT) genes are involved in the synthesis of Polymethoxyflavones. Further multi-omics analysis led to the identification of a novel OMT gene (CtgOMT1) whose transient overexpression displayed significantly higher Nobiletin content, suggesting that CtgOMT1 was involved in the synthesis of Nobiletin. Overall, our findings provide new data resources for geo-herbalism evaluation, germplasm conservation and insights into Nobiletin biosynthesis pathways for the medicinal plant C. grandis 'Tomentosa'.
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Affiliation(s)
- Lin Xian
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Liying Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yannan Fan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianhao Lin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jianmu Su
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Peng Ye
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qun Luo
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Haiyi Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaojing Lin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Caihong Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaodie Geng
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Hong Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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18
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Lu C, Pi X, Xu W, Qing P, Tang H, Li Y, Zhao Y, Liu X, Tang H, Liu Y. Clinical significance of T cell receptor repertoire in primary Sjogren's syndrome. EBioMedicine 2022; 84:104252. [PMID: 36088685 PMCID: PMC9471496 DOI: 10.1016/j.ebiom.2022.104252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/08/2022] [Accepted: 08/17/2022] [Indexed: 10/26/2022] Open
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19
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He H, Crabbe MJC, Ren Z. Detoxification Gene Families at the Genome-Wide Level of Rhus Gall Aphid Schlechtendalia chinensis. Genes (Basel) 2022; 13:1627. [PMID: 36140795 PMCID: PMC9498883 DOI: 10.3390/genes13091627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-S-transferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research.
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Affiliation(s)
- Hongli He
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - M. James C. Crabbe
- School of Life Science, Shanxi University, Taiyuan 030006, China
- Wolfson College, Oxford University, Oxford OX2 6UD, UK
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, UK
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, China
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20
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Naval-Sanchez M, Deshpande N, Tran M, Zhang J, Alhomrani M, Alsanie W, Nguyen Q, Nefzger CM. Benchmarking of ATAC Sequencing Data From BGI's Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Front Mol Biosci 2022; 9:900323. [PMID: 35874611 PMCID: PMC9302965 DOI: 10.3389/fmolb.2022.900323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Chromatin falls into one of two major subtypes: closed heterochromatin and euchromatin which is accessible, transcriptionally active, and occupied by transcription factors (TFs). The most widely used approach to interrogate differences in the chromatin state landscape is the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). While library generation is relatively inexpensive, sequencing depth requirements can make this assay cost-prohibitive for some laboratories. Findings: Here, we benchmark data from Beijing Genomics Institute's (BGI) DNBSEQ-G400 low-cost sequencer against data from a standard Illumina instrument (HiSeqX10). For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However, DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. The ability to identify master TFs that underpin the PSC state relative to fibroblasts (via HOMER, HINT-ATAC, TOBIAS), namely, foot-printing capacity, were highly similar between data generated on both platforms. Integrative analysis with transcriptional data equally enabled direct recovery of three published 3-factor combinations that have been shown to induce pluripotency. Conclusion: Other than a small increase in peak calling sensitivity for DNBSEQ-G400 data (BGI), both platforms enable comparable levels of open chromatin identification for ATAC-seq library sequencing, yielding similar analytical outcomes, albeit at low-data generation costs in the case of the BGI instrument.
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Affiliation(s)
- Marina Naval-Sanchez
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Christian M. Nefzger
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
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21
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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22
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Brealey JC, Lecaudey LA, Kodama M, Rasmussen JA, Sveier H, Dheilly NM, Martin MD, Limborg MT. Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022; 13:e0067922. [PMID: 35502903 PMCID: PMC9239044 DOI: 10.1128/mbio.00679-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.
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Affiliation(s)
- Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Laurène A. Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A. Rasmussen
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Verry AJF, Mitchell KJ, Rawlence NJ. Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa ( Emeus crassus). Biol Lett 2022; 18:20220013. [PMID: 35538842 PMCID: PMC9091836 DOI: 10.1098/rsbl.2022.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.
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Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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24
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Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K. A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.
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25
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Zhao Y, Gesang D, Wan L, Li J, Qiangba G, Danzeng W, Basang Z, Renzhen N, Yin J, Gongsang Q, Cai H, Pang H, Wang D, Asan, Zhang Q, Li J, Chen W. Echinococcus spp. and genotypes infecting humans in Tibet Autonomous Region of China: a molecular investigation with near-complete/complete mitochondrial sequences. Parasit Vectors 2022; 15:75. [PMID: 35248153 PMCID: PMC8898537 DOI: 10.1186/s13071-022-05199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Molecular markers are essential to identify Echinococcus species and genotypes in areas with multiple Echinococcus species to understand their epidemiology and pathology. Tibet Autonomous Region (TAR) is one of the areas worst hit by echinococcosis. However, molecular epidemiology is still missing among echinococcosis patients in TAR. This research explored the Echinococcus species and genotypes infecting humans in TAR and the population diversity and the possible origin of G1 in TAR. Methods Cyst samples were collected in one echinococcosis-designated hospital in TAR. Echinococcus species and genotypes were identified through a maximum-likelihood approach with near-complete/complete mtDNA using IQ-TREE. Phylogenetic networks were built with PopART, and the phylogeographical diffusion pattern was identified using a Bayesian discrete phylogeographic method. Results Using phylogenetic trees made with near-complete/complete mtDNA obtained from 92 cysts from TAR patients, the Echinococcus species and genotypes infecting humans in TAR were identified as Echinococcus granulosus (s.s.) G1 (81, 88.04%), accounting for the majority, followed by G6 of the E. canadensis cluster (6, 6.52%), E. granulosus (s.s.) G3 (3, 3.26%), and E. multilocularis (2, 2.17%). An expansion trend and a possible recent bottleneck event were confirmed among the G1 samples in TAR. Adding the other near-complete mtDNA of G1 samples globally from the literature, we identified the possible phylogeographic origin of the G1 samples in TAR as Turkey. Conclusions Using near-complete/complete mtDNA sequences of Echinococcus spp. obtained from echinococcosis patients, a variety of Echinococcus species and genotypes infecting humans throughout TAR were identified. As far as we know, this is the first comprehensive molecular investigation of Echinococcus species and genotypes infecting humans throughout TAR. We identified, for the first time to our knowledge, the possible origin of the G1 in TAR. We also enriched the long mtDNA database of Echinococcus spp. and added two complete E. multilocularis mtDNA sequences from human patients. These findings will improve our knowledge of echinococcosis, help to refine the targeted echinococcosis control measures, and serve as a valuable baseline for monitoring the Echinococcus species and genotypes mutations and trends of the Echinococcus spp. population in TAR. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05199-6.
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Affiliation(s)
- Yanping Zhao
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.,NHC Key Laboratory of Echinococcosis Prevention and Control, Lhasa, 850010, China
| | - Dunzhu Gesang
- Second People's Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Li Wan
- Second People's Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Gezhen Qiangba
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wangmu Danzeng
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Tibet, BGI-Shenzhen, Lhasa, 850000, China
| | - Zhuoga Basang
- Second People's Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Nibu Renzhen
- Second People's Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Jiefang Yin
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Quzhen Gongsang
- NHC Key Laboratory of Echinococcosis Prevention and Control, Lhasa, 850010, China.,Tibet Centre for Disease Control and Prevention, Lhasa, 850010, China
| | - Huimin Cai
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huasheng Pang
- NHC Key Laboratory of Echinococcosis Prevention and Control, Lhasa, 850010, China.,Tibet Centre for Disease Control and Prevention, Lhasa, 850010, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Asan
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Tibet, BGI-Shenzhen, Lhasa, 850000, China
| | - Qingda Zhang
- Second People's Hospital of Tibet Autonomous Region, Lhasa, 850000, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Weijun Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, 518083, China. .,BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, 518083, China.
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26
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Probing the genomic limits of de-extinction in the Christmas Island rat. Curr Biol 2022; 32:1650-1656.e3. [PMID: 35271794 PMCID: PMC9044923 DOI: 10.1016/j.cub.2022.02.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022]
Abstract
Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3, 4, 5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species. Evolutionary divergence limits the completeness of extinct species genomes The extinct Christmas Island rat was re-sequenced to ca. 60× coverage Nevertheless, 4.85% of the Norway brown rat genome remains absent after mapping Absences are not random; immune response and olfaction are excessively affected
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27
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Frias-Soler RC, Kelsey NA, Villarín Pildaín L, Wink M, Bairlein F. Transcriptome signature changes in the liver of a migratory passerine. Genomics 2022; 114:110283. [PMID: 35143886 DOI: 10.1016/j.ygeno.2022.110283] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 12/01/2022]
Abstract
The liver plays a principal role in avian migration. Here, we characterised the liver transcriptome of a long-distance migrant, the Northern Wheatear (Oenanthe oenanthe), sampled at different migratory stages, looking for molecular processes linked with adaptations to migration. The analysis of the differentially expressed genes suggested changes in the periods of the circadian rhythm, variation in the proportion of cells in G1/S cell-cycle stages and the putative polyploidization of this cell population. This may explain the dramatic increment in the liver's metabolic capacities towards migration. Additionally, genes involved in anti-oxidative stress, detoxification and innate immune responses, lipid metabolism, inflammation and angiogenesis were regulated. Lipophagy and lipid catabolism were active at all migratory stages and increased towards the fattening and fat periods, explaining the relevance of lipolysis in controlling steatosis and maintaining liver health. Our study clears the way for future functional studies regarding long-distance avian migration.
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Affiliation(s)
- Roberto Carlos Frias-Soler
- Institute of Avian Research, An der Vogelwarte 21, 26386 Wilhelmshaven, Germany; Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
| | - Natalie A Kelsey
- Institute of Avian Research, An der Vogelwarte 21, 26386 Wilhelmshaven, Germany.
| | - Lilian Villarín Pildaín
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
| | - Franz Bairlein
- Institute of Avian Research, An der Vogelwarte 21, 26386 Wilhelmshaven, Germany; Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany.
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28
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Tian R, Han K, Geng Y, Yang C, Shi C, Thomas PB, Pearce C, Moffatt K, Ma S, Xu S, Yang G, Zhou X, Gladyshev VN, Liu X, Fisher DO, Chopin LK, Leiner NO, Baker AM, Fan G, Seim I. A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. Mol Ecol Resour 2022; 22:740-754. [PMID: 34486812 PMCID: PMC9290055 DOI: 10.1111/1755-0998.13501] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy in mammals where synchronized death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report a chromosome-level genome of a male yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (Antechinus argentus and A. arktos) and the iteroparous sister species Murexia melanurus, were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.
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Affiliation(s)
- Ran Tian
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Kai Han
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | - Yuepan Geng
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Chen Yang
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | | | - Patrick B. Thomas
- Ghrelin Research GroupTranslational Research Institute‐Institute of Health and Biomedical InnovationSchool of Biomedical SciencesQueensland University of TechnologyBrisbaneQLDAustralia
- Australian Prostate Cancer Research Centre‐QueenslandTranslational Research Institute – Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
- Queensland Bladder Cancer InitiativeTranslational Research Institute‐Institute of Health and Biomedical InnovationSchool of Biomedical SciencesQueensland University of TechnologyWoolloongabbaQLDAustralia
| | - Coral Pearce
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Kate Moffatt
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Siming Ma
- Genome Institute of SingaporeAgency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMAUSA
| | - Xin Liu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | - Diana O. Fisher
- School of Biological SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Lisa K. Chopin
- Ghrelin Research GroupTranslational Research Institute‐Institute of Health and Biomedical InnovationSchool of Biomedical SciencesQueensland University of TechnologyBrisbaneQLDAustralia
- Australian Prostate Cancer Research Centre‐QueenslandTranslational Research Institute – Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
| | - Natália O. Leiner
- Laboratório de Ecologia de MamíferosInstituto de BiologiaUniversidade Federal de UberlândiaUberlândiaBrazil
| | - Andrew M. Baker
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
- Natural Environments ProgramQueensland MuseumSouth BrisbaneQLDAustralia
| | - Guangyi Fan
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Quality Research in Chinese MedicineInstitute of Chinese Medical SciencesUniversity of MacauMacauChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Inge Seim
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
- Ghrelin Research GroupTranslational Research Institute‐Institute of Health and Biomedical InnovationSchool of Biomedical SciencesQueensland University of TechnologyBrisbaneQLDAustralia
- Australian Prostate Cancer Research Centre‐QueenslandTranslational Research Institute – Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
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29
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Bergeron LA, Besenbacher S, Turner T, Versoza CJ, Wang RJ, Price AL, Armstrong E, Riera M, Carlson J, Chen HY, Hahn MW, Harris K, Kleppe AS, López-Nandam EH, Moorjani P, Pfeifer SP, Tiley GP, Yoder AD, Zhang G, Schierup MH. The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. eLife 2022; 11:73577. [PMID: 35018888 PMCID: PMC8830884 DOI: 10.7554/elife.73577] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and appropriately accounting for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a ‘Mutationathon,’ a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a twofold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria, and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.
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Affiliation(s)
- Lucie A Bergeron
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine (MOMA), Aarhus University, Aarhus N, Denmark
| | - Tychele Turner
- Department of Genetics, Washington University in St. Louis, Saint Louis, United States
| | - Cyril J Versoza
- Center for Evolution and Medicine, Arizona State University, Tempe, United States
| | - Richard J Wang
- Department of Biology, Indiana University, Bloomington, United States
| | - Alivia Lee Price
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ellie Armstrong
- Department of Biology, Stanford University, Stanford, United States
| | - Meritxell Riera
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jedidiah Carlson
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Hwei-Yen Chen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, United States
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, United States
| | | | | | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, United States
| | - George P Tiley
- Department of Biology, Duke University, Durham, United States
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, United States
| | - Guojie Zhang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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30
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Afifudeen CLW, Loh SH, Wong LL, Aziz A, Takahashi K, Wahid MEA, Cha TS. Transcriptomics de novo sequencing data of Messastrum gracile SE-MC4 under exponential and stationary growth stages. Data Brief 2021; 39:107607. [PMID: 34869809 PMCID: PMC8626828 DOI: 10.1016/j.dib.2021.107607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
Messastrum gracile SE-MC4 is a non-model microalga exhibiting superior oil-accumulating abilities. However, biomass production in M. gracile SE-MC4 is limited due to low cell proliferation especially after prolonged cultivation under oil-inducing culture conditions. Present data consist of next generation RNA sequencing data of M. gracile SE-MC4 under exponential and stationary growth stages. RNA of six samples were extracted and sequenced with insert size of 100 bp paired-end strategy using BGISEQ-500 platform to produce a total of 59.64 Gb data with 314 million reads. Sequences were filtered and de novo assembled to form 53,307 number of gene sequences. Sequencing data were deposited in National Center for Biotechnology Information (NCBI) and can be accessed via BioProject ID PRJNA552165. This information can be used to enhance biomass production in M. gracile SE-MC4 and other microalgae aimed towards improving biodiesel development.
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Affiliation(s)
- C. L. Wan Afifudeen
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Institute of Marine Biotechnology, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Saw Hong Loh
- Faculty of Science and Marine Environment, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Li Lian Wong
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Institute of Marine Biotechnology, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Ahmad Aziz
- Faculty of Science and Marine Environment, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mohd Effendy Abd Wahid
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Thye San Cha
- Faculty of Science and Marine Environment, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Satreps-Cosmos Laboratory, Central Laboratory Complex, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Corresponding author at: Faculty of Science and Marine Environment, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia.
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31
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Puetz LC, Delmont TO, Aizpurua O, Guo C, Zhang G, Katajamaa R, Jensen P, Gilbert MTP. Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:2100018. [PMID: 36619855 PMCID: PMC9744516 DOI: 10.1002/ggn2.202100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Indexed: 01/11/2023]
Abstract
Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.
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Affiliation(s)
- Lara C. Puetz
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Tom O. Delmont
- Génomique MétaboliqueGenoscopeInstitut François JacobCEACNRSUniv EvryUniversité Paris‐SaclayEvry91057France
| | - Ostaizka Aizpurua
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Chunxue Guo
- China National GeneBankBGI‐ShenzhenShenzhen518083China
| | - Guojie Zhang
- China National GeneBankBGI‐ShenzhenShenzhen518083China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagen2100Denmark
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650223China
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223China
| | - Rebecca Katajamaa
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - Per Jensen
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - M. Thomas P. Gilbert
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
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32
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Sinding MHS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey ( Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 2021; 24:103226. [PMID: 34712923 PMCID: PMC8531564 DOI: 10.1016/j.isci.2021.103226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so. We generated two genomes from the likely extinct kouprey (Bos sauveli) Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur
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Affiliation(s)
| | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jacob Agerbo Rasmussen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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33
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Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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34
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Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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35
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Zhu K, Du P, Xiong J, Ren X, Sun C, Tao Y, Ding Y, Xu Y, Meng H, Wang CC, Wen SQ. Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics. Front Genet 2021; 12:745508. [PMID: 34671385 PMCID: PMC8521044 DOI: 10.3389/fgene.2021.745508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
The MGISEQ-2000 sequencer is widely used in various omics studies, but the performance of this platform for paleogenomics has not been evaluated. We here compare the performance of MGISEQ-2000 with the Illumina X-Ten on ancient human DNA using four samples from 1750BCE to 60CE. We found there were only slight differences between the two platforms in most parameters (duplication rate, sequencing bias, θ, δS, and λ). MGISEQ-2000 performed well on endogenous rate and library complexity although X-Ten had a higher average base quality and lower error rate. Our results suggest that MGISEQ-2000 and X-Ten have comparable performance, and MGISEQ-2000 can be an alternative platform for paleogenomics sequencing.
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Affiliation(s)
- Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Panxin Du
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianxue Xiong
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Chang Sun
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yichen Tao
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Ding
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Yiran Xu
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hailiang Meng
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Institute of Archaeological Science, Fudan University, Shanghai, China
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36
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Evolutionary history of the extinct Sardinian dhole. Curr Biol 2021; 31:5571-5579.e6. [PMID: 34655517 DOI: 10.1016/j.cub.2021.09.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/23/2021] [Accepted: 09/22/2021] [Indexed: 12/30/2022]
Abstract
The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene.2-5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor.3,6-9 Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca-21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids-probably a result of the long-term isolation-that could have contributed to the subsequent extinction of the Sardinian dhole.
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37
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Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021; 184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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Affiliation(s)
- Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | - Michael V Westbury
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - David A Duchêne
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Fátima Sánchez-Barreiro
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Remi André-Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Binia De Cahsan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guanliang Meng
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Chentao Yang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa
| | - Kees Rookmaaker
- Editor of the Rhino Resource Center, Utrecht, the Netherlands
| | - Michael W Bruford
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK
| | - Oliver Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | | | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Chunxue Guo
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow 119017, Russia
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Robert R Dunn
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Eline D Lorenzen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA
| | - Guojie Zhang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway.
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38
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Johnson-Weaver BT, Choi HW, Yang H, Granek JA, Chan C, Abraham SN, Staats HF. Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens. Front Immunol 2021; 12:730346. [PMID: 34566991 PMCID: PMC8461742 DOI: 10.3389/fimmu.2021.730346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 01/02/2023] Open
Abstract
Mast cell activators are a novel class of mucosal vaccine adjuvants. The polymeric compound, Compound 48/80 (C48/80), and cationic peptide, Mastoparan 7 (M7) are mast cell activators that provide adjuvant activity when administered by the nasal route. However, small molecule mast cell activators may be a more cost-efficient adjuvant alternative that is easily synthesized with high purity compared to M7 or C48/80. To identify novel mast cell activating compounds that could be evaluated for mucosal vaccine adjuvant activity, we employed high-throughput screening to assess over 55,000 small molecules for mast cell degranulation activity. Fifteen mast cell activating compounds were down-selected to five compounds based on in vitro immune activation activities including cytokine production and cellular cytotoxicity, synthesis feasibility, and selection for functional diversity. These small molecule mast cell activators were evaluated for in vivo adjuvant activity and induction of protective immunity against West Nile Virus infection in BALB/c mice when combined with West Nile Virus envelope domain III (EDIII) protein in a nasal vaccine. We found that three of the five mast cell activators, ST101036, ST048871, and R529877, evoked high levels of EDIII-specific antibody and conferred comparable levels of protection against WNV challenge. The level of protection provided by these small molecule mast cell activators was comparable to the protection evoked by M7 (67%) but markedly higher than the levels seen with mice immunized with EDIII alone (no adjuvant 33%). Thus, novel small molecule mast cell activators identified by high throughput screening are as efficacious as previously described mast cell activators when used as nasal vaccine adjuvants and represent next-generation mast cell activators for evaluation in mucosal vaccine studies.
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Affiliation(s)
| | - Hae Woong Choi
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
| | - Hang Yang
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Josh A. Granek
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Cliburn Chan
- Biostatistics and Bioinformatics Department, School of Medicine, Duke University, Durham, NC, United States
| | - Soman N. Abraham
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
- Department of Immunology, School of Medicine, Duke University, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
| | - Herman F. Staats
- Pathology Department, School of Medicine, Duke University, Durham, NC, United States
- Department of Immunology, School of Medicine, Duke University, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
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39
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Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Mol Ecol 2021; 30:6355-6369. [PMID: 34176179 PMCID: PMC9291831 DOI: 10.1111/mec.16043] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023]
Abstract
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,DTU Bioinformatics, Kongens Lyngby, Hovedstaden, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Ashot Margaryan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Marta M Ciucani
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Zena Timmons
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Thomas Sicheritz-Pontén
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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40
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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41
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Margaryan A, Sinding MS, Carøe C, Yamshchikov V, Burtsev I, Gilbert MTP. The genomic origin of Zana of Abkhazia. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10051. [PMID: 36618122 PMCID: PMC9744565 DOI: 10.1002/ggn2.10051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/13/2021] [Indexed: 01/11/2023]
Abstract
Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.
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Affiliation(s)
- Ashot Margaryan
- Section for Evolutionary Genomics, GLOBE InstituteFaculty of Health and Medical Sciences University of CopenhagenCopenhagenDenmark
- Center for Evolutionary HologenomicsUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel‐Holger S. Sinding
- Section for Evolutionary Genomics, GLOBE InstituteFaculty of Health and Medical Sciences University of CopenhagenCopenhagenDenmark
- Smurfit Institute of GeneticsTrinity College DublinDublinIreland
| | - Christian Carøe
- Section for Evolutionary Genomics, GLOBE InstituteFaculty of Health and Medical Sciences University of CopenhagenCopenhagenDenmark
| | | | - Igor Burtsev
- International Center of HominologyState Darwin MuseumMoscowRussia
| | - M. Thomas P. Gilbert
- Center for Evolutionary HologenomicsUniversity of CopenhagenCopenhagenDenmark
- Department of Natural HistoryNTNUTrondheimNorway
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42
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Hofreiter M, Sneberger J, Pospisek M, Vanek D. Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. Forensic Sci Int Genet 2021; 54:102538. [PMID: 34265517 DOI: 10.1016/j.fsigen.2021.102538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/07/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.
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Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Jiri Sneberger
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic.
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43
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Kapp JD, Green RE, Shapiro B. A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA. J Hered 2021; 112:241-249. [PMID: 33768239 PMCID: PMC8141684 DOI: 10.1093/jhered/esab012] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/12/2022] Open
Abstract
We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina’s P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.
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Affiliation(s)
- Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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44
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Li P, Wang K, Qiu S, Lin Y, Xie J, Li J, Li L, Jia L, Jiang Y, Li P, Song H. Rapid identification and metagenomics analysis of the adenovirus type 55 outbreak in Hubei using real-time and high-throughput sequencing platforms. INFECTION GENETICS AND EVOLUTION 2021; 93:104939. [PMID: 34029726 DOI: 10.1016/j.meegid.2021.104939] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022]
Abstract
The rise in human adenovirus (HAdV) infections poses a serious challenge to public health in China. Real-time (RT) sequencing provides solutions for achieving rapid pathogen identification during outbreaks, whereas high-throughput sequencing yields higher sequence accuracy. In the present study, we report the outcomes of applying nanopore and BGI platforms in the identification and genomic analysis of an HAdV outbreak in Hubei province, China in May of 2019. A mixed sample of nine nasopharyngeal swabs and one single sample were submitted to direct nanopore sequencing (MinION device), generating their first HAdV-55 reads within 13 and 20 min, respectively. The sequences were confirmed by RT-polymerase chain reaction (PCR). Ten HAdV-positive samples were further sequenced using next-generation high-throughput sequencing (BGISEQ-500 device). Phylogenetic analysis revealed that the outbreak strain had a close genetic relation to strains isolated in Sichuan province. Metagenomic analysis showed that HAdV-55 was not a dominant species in samples from which the whole HAdV-55 genome could not be assembled. The present results highlight the value of combining sequencing platforms and using mixed samples for nucleic acid enrichment in pathogen detection of infectious disease outbreaks.
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Affiliation(s)
- Peihan Li
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shaofu Qiu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jing Xie
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lizhong Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yongqiang Jiang
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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45
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Chua PYS, Crampton-Platt A, Lammers Y, Alsos IG, Boessenkool S, Bohmann K. Metagenomics: A viable tool for reconstructing herbivore diet. Mol Ecol Resour 2021; 21:2249-2263. [PMID: 33971086 PMCID: PMC8518049 DOI: 10.1111/1755-0998.13425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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Affiliation(s)
- Physilia Y S Chua
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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46
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Transcriptional Landscape of Vero E6 Cells during Early Swine Acute Diarrhea Syndrome Coronavirus Infection. Viruses 2021; 13:v13040674. [PMID: 33919952 PMCID: PMC8070899 DOI: 10.3390/v13040674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 01/17/2023] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly emerged and highly pathogenic virus that is associated with fatal diarrhea disease in piglets, causing significant economic losses to the pig industry. At present, the research on the pathogenicity and molecular mechanisms of host-virus interactions of SADS-CoV are limited and remain poorly understood. Here, we investigated the global gene expression profiles of SADS-CoV-infected Vero E6 cells at 12, 18, and 24 h post-infection (hpi) using the RNA-sequencing. As a result, a total of 3324 differentially expressed genes (DEG) were identified, most of which showed a down-regulated expression pattern. Functional enrichment analyses indicated that the DEGs are mainly involved in signal transduction, cellular transcription, immune and inflammatory response, and autophagy. Collectively, our results provide insights into the changes in the cellular transcriptome during early infection of SADS-CoV and may provide information for further study of molecular mechanisms.
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47
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Sun X, Hu YH, Wang J, Fang C, Li J, Han M, Wei X, Zheng H, Luo X, Jia Y, Gong M, Xiao L, Song Z. Efficient and stable metabarcoding sequencing data using a DNBSEQ-G400 sequencer validated by comprehensive community analyses. GIGABYTE 2021; 2021:gigabyte16. [PMID: 36824325 PMCID: PMC9632034 DOI: 10.46471/gigabyte.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
Metabarcoding is a widely used method for fast characterization of microbial communities in complex environmental samples. However, the selction of sequencing platform can have a noticeable effect on the estimated community composition. Here, we evaluated the metabarcoding performance of a DNBSEQ-G400 sequencer developed by MGI Tech using 16S and internal transcribed spacer (ITS) markers to investigate bacterial and fungal mock communities, as well as the ITS2 marker to investigate the fungal community of 1144 soil samples, with additional technical replicates. We show that highly accurate sequencing of bacterial and fungal communities is achievable using DNBSEQ-G400. Measures of diversity and correlation from soil metabarcoding showed that the results correlated highly with those of different machines of the same model, as well as between different sequencing modes (single-end 400 bp and paired-end 200 bp). Moderate, but significant differences were observed between results produced with different sequencing platforms (DNBSEQ-G400 and MiSeq); however, the highest differences can be caused by selecting different primer pairs for PCR amplification of taxonomic markers. These differences suggested that care is needed while jointly analyzing metabarcoding data from differenet experiments. This study demonstrated the high performance and accuracy of DNBSEQ-G400 for short-read metabarcoding of microbial communities. Our study also produced datasets to allow further investigation of microbial diversity.
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Affiliation(s)
| | - Yue-Hua Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | | | - Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiguang Li
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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48
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Tu C, Li H, Liu X, Wang Y, Li W, Meng L, Wang W, Li Y, Li D, Du J, Lu G, Lin G, Tan YQ. TDRD7 participates in lens development and spermiogenesis by mediating autophagosome maturation. Autophagy 2021; 17:3848-3864. [PMID: 33618632 DOI: 10.1080/15548627.2021.1894058] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In humans, TDRD7 (tudor domain containing 7) mutations lead to a syndrome combining congenital cataracts (CCs) and non-obstructive azoospermia (NOA), characterized by abnormal lens development and spermiogenesis. However, the molecular mechanism underlying TDRD7's functions in eye and testicular development are still largely unknown. Here, we show that the depletion of this gene in mice and humans resulted in the accumulation of autophagosomes and the disruption of macroautophagic/autophagic flux. The disrupted autophagic flux in tdrd7-deficient mouse embryonic fibroblasts (MEFs) was caused by a failure of autophagosome fusion with lysosomes. Furthermore, transcriptome analysis and biochemical assays showed that TDRD7 might directly bind to Tbc1d20 mRNAs and downregulate its expression, which is a key regulator of autophagosome maturation, resulting in the disruption of autophagosome maturation. In addition, we provide evidence to show that TDRD7-mediated autophagosome maturation maintains lens transparency by facilitating the removal of damaged proteins and organelles from lens fiber cells and the biogenesis of acrosome. Altogether, our results showed that TDRD7 plays an essential role in the maturation of autophagosomes and that tdrd7 deletion results in eye defects and testicular abnormalities in mice, implicating disrupted autophagy might be the mechanism that contributes to lens development and spermiogenesis defects in human.Abbreviations: CB: chromatoid bodies; CC: congenital cataract; CTSD: cathepsin D; DMSO: dimethyl sulfoxide; LAMP1: lysosomal-associated membrane protein 1; LECs: lens epithelial cells; MAP1LC3/LC3/Atg8: microtubule-associated protein 1 light chain 3; MEFs: mouse embryonic fibroblasts; NOA: non-obstructive azoospermia; OFZ: organelle-free zone; RG: RNA granules; SQSTM1/p62: sequestosome 1; TBC1D20: TBC1 domain family member 20; TDRD7: tudor domain containing 7; TEM: transmission electron microscopy; WT: wild type.
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Affiliation(s)
- Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Haiyu Li
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Xuyang Liu
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, Jinan University, Shenzhen, China
| | - Ying Wang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lanlan Meng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Yong Li
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Dongyan Li
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
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49
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Single-cell RNA-seq reveals novel mitochondria-related musculoskeletal cell populations during adult axolotl limb regeneration process. Cell Death Differ 2021; 28:1110-1125. [PMID: 33116295 PMCID: PMC7937690 DOI: 10.1038/s41418-020-00640-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 01/30/2023] Open
Abstract
While the capacity to regenerate tissues or limbs is limited in mammals, including humans, axolotls are able to regrow entire limbs and major organs after incurring a wound. The wound blastema has been extensively studied in limb regeneration. However, due to the inadequate characterization of ECM and cell subpopulations involved in the regeneration process, the discovery of the key drivers for human limb regeneration remains unknown. In this study, we applied large-scale single-cell RNA sequencing to classify cells throughout the adult axolotl limb regeneration process, uncovering a novel regeneration-specific mitochondria-related cluster supporting regeneration through energy providing and the ECM secretion (COL2+) cluster contributing to regeneration through cell-cell interactions signals. We also discovered the dedifferentiation and re-differentiation of the COL1+/COL2+ cellular subpopulation and exposed a COL2-mitochondria subcluster supporting the musculoskeletal system regeneration. On the basis of these findings, we reconstructed the dynamic single-cell transcriptome of adult axolotl limb regenerative process, and identified the novel regenerative mitochondria-related musculoskeletal populations, which yielded deeper insights into the crucial interactions between cell clusters within the regenerative microenvironment.
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50
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dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
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