51
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Malekmohammadi L, Sheidai M, Ghahremaninejad F, Danehkar A, Koohdar F. Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches. BMC Plant Biol 2023; 23:459. [PMID: 37789283 PMCID: PMC10546741 DOI: 10.1186/s12870-023-04475-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.
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Affiliation(s)
- Laleh Malekmohammadi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Masoud Sheidai
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Farrokh Ghahremaninejad
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Afshin Danehkar
- Department of Environmental Sciences, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Fahimeh Koohdar
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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Rodriguez D, Harding SF, Sirsi S, McNichols-O’Rourke K, Morris T, Forstner MRJ, Schwalb AN. Mitochondrial sequence data reveal population structure within Pustulosa pustulosa. PeerJ 2023; 11:e15974. [PMID: 37810794 PMCID: PMC10552767 DOI: 10.7717/peerj.15974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/06/2023] [Indexed: 10/10/2023] Open
Abstract
Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.
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Affiliation(s)
- David Rodriguez
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Stephen F. Harding
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Shashwat Sirsi
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Kelly McNichols-O’Rourke
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | - Todd Morris
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, ON, Canada
| | | | - Astrid N. Schwalb
- Department of Biology, Texas State University, San Marcos, TX, United States
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Li P, Xiao L, Du Q, Quan M, Song Y, He Y, Huang W, Xie J, Lv C, Wang D, Zhou J, Li L, Liu Q, El‐Kassaby YA, Zhang D. Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. Plant Biotechnol J 2023; 21:2002-2018. [PMID: 37392407 PMCID: PMC10502748 DOI: 10.1111/pbi.14108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.
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Affiliation(s)
- Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuepeng Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuling He
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Weixiong Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Dan Wang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qing Liu
- CSIRO Agriculture and Food, Black MountainCanberraAustralian Capital TerritoryAustralia
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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Furtado LFV, de Miranda RRC, Tennessen JA, Blouin MS, Rabelo ÉML. Molecular variability of the Ancylostoma secreted Protein-2 (Aca-asp-2) gene from Ancylostoma caninum contributes to expand information on population genetic studies of hookworms. Exp Parasitol 2023; 253:108590. [PMID: 37544398 DOI: 10.1016/j.exppara.2023.108590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Hookworm infection is a major public health problem in many regions of the world. Given the high levels of host morbidity and even mortality of the host caused by these infections, it is crucial to understand the genetic structure of hookworm populations. This understanding can provide insights into the ecology, transmission patterns, mechanisms of drug resistance, and the development of vaccines and immunotherapeutic strategies. Previously, we examined presumably neutral molecular markers, such as microsatellites and COI (Cytochrome C oxidase subunit 1) in Brazilian populations of Ancylostoma caninum. Here we analyze the molecular variability of a genomic fragment of the Aca-asp-2 (Ancylostoma secreted protein-2) gene from Ancylostoma caninum. This gene is a highly expressed and activated following the infection of the L3 larvae in the host. We obtained individuals of A. caninum from five different geographic locations in Brazil, sequenced and analyzed parts of the gene. The results revealed extensive polymorphism at this fragment, especially in the intronic region, indicating low selective pressure acting on these sequences. However, we also observed irregular distributions of nucleotides and polymorphisms in the coding region of this gene, resulting in the identification of 27 alleles. The data presented here contribute to expanding the understanding of population genetic studies of hookworms.
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Affiliation(s)
- Luis Fernando Viana Furtado
- Universidade Federal de Minas Gerais, Faculdade de Farmácia, Departamento de Análises Clínicas e Toxicológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
| | - Rodrigo Rodrigues Cambraia de Miranda
- Universidade Federal de Uberlândia, Instituto de Ciências Biomédicas, Avenida Maranhão, 1783, Umuarama, CEP 38405-318, Uberlândia, Minas Gerais, Brazil
| | | | | | - Élida Mara Leite Rabelo
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
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Washington AM, Foss K, Krause JH, Davis AM, Kuczynski KJ, Milko LV, Berg JS, Roberts MC. Consideration of the Beneficiary Inducement Statute on Access to Health Care Systems' Population Genetic Screening Programs. Public Health Genomics 2023; 26:183-187. [PMID: 37778346 PMCID: PMC10619584 DOI: 10.1159/000534365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Affiliation(s)
- Aurora M. Washington
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kimberly Foss
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joan H. Krause
- School of Law, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arlene M. Davis
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristine J. Kuczynski
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura V. Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan C. Roberts
- School of Pharmacy – Division of Pharmaceutical Outcomes and Policy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Yang X, Mao Y, Wang XK, Ma DN, Xu Z, Gong N, Henning B, Zhang X, He G, Shi YY, Eichler EE, Li ZQ, Takahashi E, Li WD. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zool Res 2023; 44:837-847. [PMID: 37501399 PMCID: PMC10559097 DOI: 10.24272/j.issn.2095-8137.2022.514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
The common marmoset ( Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 ( PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
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Affiliation(s)
- XiangYu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - YaFei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xuan-Kai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dong-Ni Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Zhen Xu
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Neng Gong
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Barbara Henning
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xu Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong-Yong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle WA 98195, USA
| | - Zhi-Qiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China. E-mail:
| | - Eiki Takahashi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan. E-mail:
| | - Wei-Dong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
- Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai 200240, China. E-mail:
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Yu Z, Fidler TP, Ruan Y, Vlasschaert C, Nakao T, Uddin MM, Mack T, Niroula A, Heimlich JB, Zekavat SM, Gibson CJ, Griffin GK, Wang Y, Peloso GM, Heard-Costa N, Levy D, Vasan RS, Aguet F, Ardlie KG, Taylor KD, Rich SS, Rotter JI, Libby P, Jaiswal S, Ebert BL, Bick AG, Tall AR, Natarajan P. Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk. J Clin Invest 2023; 133:e168597. [PMID: 37498674 PMCID: PMC10503804 DOI: 10.1172/jci168597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is associated with an increased risk of cardiovascular diseases (CVDs), putatively via inflammasome activation. We pursued an inflammatory gene modifier scan for CHIP-associated CVD risk among 424,651 UK Biobank participants. We identified CHIP using whole-exome sequencing data of blood DNA and modeled as a composite, considering all driver genes together, as well as separately for common drivers (DNMT3A, TET2, ASXL1, and JAK2). We developed predicted gene expression scores for 26 inflammasome-related genes and assessed how they modify CHIP-associated CVD risk. We identified IL1RAP as a potential key molecule for CHIP-associated CVD risk across genes and increased AIM2 gene expression leading to heightened JAK2- and ASXL1-associated CVD risk. We show that CRISPR-induced Asxl1-mutated murine macrophages had a particularly heightened inflammatory response to AIM2 agonism, associated with an increased DNA damage response, as well as increased IL-10 secretion, mirroring a CVD-protective effect of IL10 expression in ASXL1 CHIP. Our study supports the role of inflammasomes in CHIP-associated CVD and provides evidence to support gene-specific strategies to address CHIP-associated CVD risk.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Trevor P. Fidler
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Yunfeng Ruan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Tetsushi Nakao
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Taralynn Mack
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - J. Brett Heimlich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seyedeh M. Zekavat
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Institute, Boston, Massachusetts, USA
| | - Christopher J. Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gabriel K. Griffin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Nancy Heard-Costa
- Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts, USA
- Division of Intramural Research, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Ramachandran S. Vasan
- Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Siddhartha Jaiswal
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin L. Ebert
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander G. Bick
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan R. Tall
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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59
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Gstöttenmayer F, Moyaba P, Rodriguez M, Mulandane FC, Mucache HN, Neves L, De Beer C, Ravel S, De Meeûs T, Mach RL, Vreysen MJB, Abd-Alla AM. Development and characterization of microsatellite markers for the tsetse species Glossina brevipalpis and preliminary population genetics analyses. Parasite 2023; 30:34. [PMID: 37712836 PMCID: PMC10503490 DOI: 10.1051/parasite/2023038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
Tsetse flies, the vectors of African trypanosomes are of key medical and economic importance and one of the constraints for the development of Africa. Tsetse fly control is one of the most effective and sustainable strategies used for controlling the disease. Knowledge about population structure and level of gene flow between neighbouring populations of the target vector is of high importance to develop appropriate strategies for implementing effective management programmes. Microsatellites are commonly used to identify population structure and assess dispersal of the target populations and have been developed for several tsetse species but were lacking for Glossina brevipalpis. In this study, we screened the genome of G. brevipalpis to search for suitable microsatellite markers and nine were found to be efficient enough to distinguish between different tsetse populations. The availability of these novel microsatellite loci will help to better understand the population biology of G. brevipalpis and to assess the level of gene flow between different populations. Such information will help with the development of appropriate strategies to implement the sterile insect technique (SIT) in the framework of an area-wide integrated pest management (AW-IPM) approach to manage tsetse populations and ultimately address the trypanosomoses problem in these targeted areas.
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Affiliation(s)
- Fabian Gstöttenmayer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Percy Moyaba
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary Research 100 Soutpan Road Private Bag X05 Onderstepoort 0110 South Africa
| | - Montse Rodriguez
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Fernando C. Mulandane
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
| | - Hermógenes N. Mucache
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
| | - Luis Neves
- University Eduardo Mondlane, Centro de Biotecnologia Av. de Moçambique Km 1.5 Maputo Mozambique
- University of Pretoria, Department of Veterinary Tropical Diseases Private Bag X04 Onderstepoort 0110 South Africa
| | - Chantel De Beer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Sophie Ravel
- University of Montpellier, Cirad, IRD, Intertryp Campus International de Baillarguet 34398 Montpellier Cedex 5 France
| | - Thierry De Meeûs
- University of Montpellier, Cirad, IRD, Intertryp Campus International de Baillarguet 34398 Montpellier Cedex 5 France
| | - Robert L. Mach
- Institute of Chemical, Environmental, and Bioscience Engineering, Vienna University of Technology Gumpendorfer Straße 1a 1060 Vienna Austria
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
| | - Adly M.M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna International Centre P.O. Box 100 1400 Vienna Austria
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60
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García-Olivares V, Muñoz-Barrera A, Rubio-Rodríguez LA, Jáspez D, Díaz-de Usera A, Iñigo-Campos A, Veeramah KR, Alonso S, Thomas MG, Lorenzo-Salazar JM, González-Montelongo R, Flores C. Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data. Comput Struct Biotechnol J 2023; 21:4613-4618. [PMID: 37817776 PMCID: PMC10560978 DOI: 10.1016/j.csbj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Krishna R. Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, United States
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- María Goyri Building, Biotechnology Center, Human Molecular Evolution Lab 2.08 UPV/EHU Science Park, 48940 Leioa, Bizkaia, Spain
| | - Mark G. Thomas
- UCL Genetics Institute, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom
- Research Department of Genetics, Evolution & Environment, University College London (UCL), Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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Diesel J, Molano G, Montecinos GJ, DeWeese K, Calhoun S, Kuo A, Lipzen A, Salamov A, Grigoriev IV, Reed DC, Miller RJ, Nuzhdin SV, Alberto F. A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera). BMC Genomics 2023; 24:543. [PMID: 37704968 PMCID: PMC10498591 DOI: 10.1186/s12864-023-09658-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp's economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
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Affiliation(s)
- Jose Diesel
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Gabriel J Montecinos
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kelly DeWeese
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sara Calhoun
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Daniel C Reed
- Marine Science Institute, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Robert J Miller
- Marine Science Institute, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sergey V Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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Kaur K, Rinaldo A, Lovelock D, Rodoni B, Constable F. The genetic variability of grapevine Pinot gris virus (GPGV) in Australia. Virol J 2023; 20:211. [PMID: 37705082 PMCID: PMC10500770 DOI: 10.1186/s12985-023-02171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Grapevine Pinot gris virus (GPGV; genus Trichovirus in the family Betaflexiviridae) was detected in Australia in 2016, but its impact on the production of nursery material and fruit in Australia is still currently unknown. This study investigated the prevalence and genetic diversity of GPGV in Australia. GPGV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in a range of rootstock, table and wine grape varieties from New South Wales, South Australia, and Victoria, with 473/2171 (21.8%) samples found to be infected. Genomes of 32 Australian GPGV isolates were sequenced and many of the isolates shared high nucleotide homology. Phylogenetic and haplotype analyses demonstrated that there were four distinct clades amongst the 32 Australian GPGV isolates and that there were likely to have been at least five separate introductions of the virus into Australia. Recombination and haplotype analysis indicate the emergence of new GPGV strains after introduction into Australia. When compared with 168 overseas GPGV isolates, the analyses suggest that the most likely origin of Australian GPGV isolates is from Europe. There was no correlation between specific GPGV genotypes and symptoms such as leaf mottling, leaf deformation, and shoot stunting, which were observed in some vineyards, and the virus was frequently found in symptomless grapevines.
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Affiliation(s)
- Kamalpreet Kaur
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, Melbourne, VIC, Australia.
| | - Amy Rinaldo
- The Australian Wine Research Institute, Adelaide, SA, Australia
| | - David Lovelock
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, Melbourne, VIC, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, Melbourne, VIC, Australia
| | - Fiona Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, Melbourne, VIC, Australia
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Laso-Jadart R, O'Malley M, Sykulski AM, Ambroise C, Madoui MA. Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations. BMC Ecol Evol 2023; 23:46. [PMID: 37658324 PMCID: PMC10472650 DOI: 10.1186/s12862-023-02160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method. RESULTS We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors. CONCLUSION Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.
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Affiliation(s)
- Romuald Laso-Jadart
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France
| | - Michael O'Malley
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Adam M Sykulski
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France.
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-Aux-Roses, France.
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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Ni R, Wang Y, Zhong Q, Li M, Zhang D, Zhang Y, Qiu X. Absence of known knockdown resistance mutations but fixation of CYP337B3 was detected in field populations of Helicoverpa armigera across China. Pestic Biochem Physiol 2023; 195:105542. [PMID: 37666613 DOI: 10.1016/j.pestbp.2023.105542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
The cotton bollworm (Helicoverpa armigera) is a worldwide agricultural pest that infests many important crops. Pyrethroids targeting the voltage-gated sodium channel (VGSC) have been long used in the control of the cotton bollworm. Two amino acid substitutions (D1561V and E1565G) in H. armigera VGSC (HaVGSC) and the presence of a chimeric P450 gene (CYP337B3) have been documented to be associated with pyrethroid resistance. To understand the current occurrence of kdr mutations and the CYP337B3 gene in Chinese H. armigera populations, high-throughput amplicon sequencing was adopted to detect potential nucleotide variations in three fragments of the VGSC gene that cover 10 reported knockdown resistance (kdr) sites in insects, and gene-specific PCR was performed to examine the presence of CYP337B3 gene in H. armigera samples collected across China. The nucleotide variation analysis revealed a wealth of nucleotide variations in not only exons but also introns in the VGSC gene in Chinese H. armigera populations. However, neither previously reported kdr-conferring amino acid replacements nor other non-synonymous mutations were observed in a total of 1439 examined individuals. Population genetic analysis suggested that the H. armigera population in Nanchang, Jiangxi Province (JNC) had a moderate genetic differentiation from other populations, while no significant divergence was observed in other populations in northern and northwestern China. The CYP337B3 was present in all the examined individuals, indicating that CYP337B3 is extensively fixed in H. armigera populations across China. These results support that point mutations in VGSC are not a major factor involved in the current pyrethroid resistance in H. armigera. Instead, CYP337B3 plays a prevalent role in the development of resistance to pyrethroids in H. armigera.
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Affiliation(s)
- Ruoyao Ni
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yawei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiuzan Zhong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Ganzhou Vegetable and Flower Research Institute, Ganzhou, Jiangxi Province 341413, China.
| | - Mei Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dandan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xinghui Qiu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Fiesinger A, Held C, Melzner F, Putchim L, Reusch TBH, Schmidt AL, Wall M. Population genetic differentiation of the ubiquitous brooding coral Pocillopora acuta along Phuket Island reefs in the Andaman Sea, Thailand. BMC Ecol Evol 2023; 23:42. [PMID: 37626296 PMCID: PMC10464487 DOI: 10.1186/s12862-023-02153-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The widespread Indo-Pacific coral species Pocillopora acuta Lamarck, 1816 displays varying levels of asexual versus sexual reproduction, with strong repercussions on genetic diversity, connectivity and genetic structuring within and among populations. For many geographic regions, baseline information on genetic diversity is still lacking, particularly in the Andaman Sea. The region suffered a massive heat-induced bleaching event in 2010 with high coral cover loss of branching coral species such as P. acuta. A subsequent bleaching in 2016, however, revealed a mild bleaching response in pocilloporids compared to other coral taxa in the region, suggesting that rare, heat tolerant genotypes had been selected by the 2010 bleaching event. In order to test whether this potential 'evolutionary rescue' event has led to a low genetic diversity, we conducted a population genetic survey covering a total of nine different P. acuta populations (336 individuals) along a 50 km coastal stretch around Phuket Island, Thailand. We used six microsatellite markers to assess genotypic diversity and to determine the prevalent mode of reproduction (i.e. sexual or asexual recruitment). RESULTS In contrast to other Indian Ocean P. acuta populations, the majority of corals in this study adopted a sexual reproduction mode (75% across all populations). At the same time, substantial regional gene flow was observed around Phuket Island with strong genetic differentiation as indicated by three genetic clusters that were separated by only a few kilometers. Patterns of isolation by distance over 0.7 - 40 km suggest small-scale genetic barriers, such as changing currents throughout each monsoonal season, potentially contributing to locally restricted dispersal of P. acuta larvae. CONCLUSIONS The occurrence of distinct genetic clusters within short coastal stretches suggests that the 2010 bleaching event has not led to extreme genetic impoverishment. While more in-depth genomic analyses are necessary to investigate changes in genetic diversity following extreme bleaching events, our results will help guide conservation efforts to maintain genetic diversity of a coral species that likely will be dominant in future, warmer Andaman Sea reefs.
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Affiliation(s)
- Anna Fiesinger
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany.
- Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78464, Germany.
| | - Christoph Held
- Alfred-Wegener-Institut, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Lalita Putchim
- Phuket Marine Biological Centre, Wichit, Phuket, Mueang Phukt District, 83000, Thailand
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine Evolutionary Ecoloy, Wischhofstraße 1-3, Kiel, 24148, Germany
| | - Andrea L Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany
- Cooperative Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Marlene Wall
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Experimental Ecology - Benthic Ecology, Wischhofstraße 1-3, 24148, Kiel, Germany.
- Alfred-Wegener-Institut, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany.
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Wu CHW, Badreddine J, Chang J, Huang YRM, Kim FJ, Wild T, Tsai ACH, Meeks N, Donalisio Da Silva R, Molina WR, Schumacher FR. Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain. Urolithiasis 2023; 51:101. [PMID: 37561200 DOI: 10.1007/s00240-023-01473-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Cystine stone is a Mendelian genetic disease caused by SLC3A1 or SLC7A9. In this study, we aimed to estimate the genetic prevalence of cystine stones and compare it with the clinical prevalence to better understand the disease etiology. METHODS We analyzed genetic variants in the general population using the 1000 Genomes project and the Human Gene Mutation Database to extract all SLC3A1 and SLC7A9 pathogenic variants. All variants procured from both databases were intersected. Pathogenic allele frequency, carrier rate, and affected rate were calculated and estimated based on Hardy-Weinberg equilibrium. RESULTS We found that 9 unique SLC3A1 pathogenic variants were carried by 26 people and 5 unique SLC7A9 pathogenic variants were carried by 12 people, all of whom were heterozygote carriers. No homozygote, compoun d heterozygote, or double heterozygote was identified in the 1000 Genome database. Based on the Hardy-Weinberg equilibrium, the calculated genetic prevalence of cystine stone disease is 1 in 30,585. CONCLUSION The clinical prevalence of cystine stone has been previously reported as 1 in 7,000, a notably higher figure than the genetic prevalence of 1 in 30,585 calculated in this study. This suggests that the etiology of cystine stone is more complex than what our current genetic knowledge can explain. Possible factors that may contribute to this difference include novel causal genes, undiscovered pathogenic variants, alternative inheritance models, founder effects, epigenetic modifications, environmental factors, or other modifying factors. Further investigation is needed to fully understand the etiology of cystine stone.
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Affiliation(s)
- Chen-Han Wilfred Wu
- Department of Genetics and Genome Sciences, Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, OH, USA.
| | - Jad Badreddine
- Department of Genetics and Genome Sciences, Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, OH, USA
| | - Joshua Chang
- Department of Genetics and Genome Sciences, Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, OH, USA
| | - Yu-Ren Mike Huang
- Department of Genetics and Genome Sciences, Department of Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, OH, USA
| | - Fernando J Kim
- Division of Urology, Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Trevor Wild
- Division of Urology, Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anne Chun-Hui Tsai
- Section of Genetics, Department of Pediatrics, University of Illinois Chicago, Chicago, IL, USA
| | - Naomi Meeks
- Division of Clinical Genetics and Metabolism, Department of Pediatrics, Children's Hospital Colorado, University of Colorado, Aurora, CO, USA
| | | | - Wilson R Molina
- Department of Urology, School of Medicine, University of Kansas, Kansas City, KS, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Odero JO, Nambunga IH, Wangrawa DW, Badolo A, Weetman D, Koekemoer LL, Ferguson HM, Okumu FO, Baldini F. Advances in the genetic characterization of the malaria vector, Anopheles funestus, and implications for improved surveillance and control. Malar J 2023; 22:230. [PMID: 37553665 PMCID: PMC10410966 DOI: 10.1186/s12936-023-04662-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Anopheles mosquitoes present a major public health challenge in sub-Saharan Africa; notably, as vectors of malaria that kill over half a million people annually. In parts of the east and southern Africa region, one species in the Funestus group, Anopheles funestus, has established itself as an exceptionally dominant vector in some areas, it is responsible for more than 90% of all malaria transmission events. However, compared to other malaria vectors, the species is far less studied, partly due to difficulties in laboratory colonization and the unresolved aspects of its taxonomy and systematics. Control of An. funestus is also increasingly difficult because it has developed widespread resistance to public health insecticides. Fortunately, recent advances in molecular techniques are enabling greater insights into species identity, gene flow patterns, population structure, and the spread of resistance in mosquitoes. These advances and their potential applications are reviewed with a focus on four research themes relevant to the biology and control of An. funestus in Africa, namely: (i) the taxonomic characterization of different vector species within the Funestus group and their role in malaria transmission; (ii) insecticide resistance profile; (iii) population genetic diversity and gene flow, and (iv) applications of genetic technologies for surveillance and control. The research gaps and opportunities identified in this review will provide a basis for improving the surveillance and control of An. funestus and malaria transmission in Africa.
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Affiliation(s)
- Joel O Odero
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania.
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Ismail H Nambunga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Dimitri W Wangrawa
- Laboratoire d'Entomologie Fondamentale et Appliquée, Université Joseph ZEBRO, Ouagadougou, Burkina Faso
| | - Athanase Badolo
- Laboratoire d'Entomologie Fondamentale et Appliquée, Université Joseph ZEBRO, Ouagadougou, Burkina Faso
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic Parasitic Diseases, Vector Control Reference Laboratory, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Heather M Ferguson
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- School of Life Science and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Francesco Baldini
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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Zhong ZP, Vik D, Rapp JZ, Zablocki O, Maughan H, Temperton B, Deming JW, Sullivan MB. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. Microbiome 2023; 11:174. [PMID: 37550784 PMCID: PMC10405475 DOI: 10.1186/s40168-023-01619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. RESULTS We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. CONCLUSIONS Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Dean Vik
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Josephine Z Rapp
- Department of Biology, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, UK
| | - Jody W Deming
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, WA, USA.
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
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Tsukagoshi H, Abe S. Isolation and characterization of 17 polymorphic microsatellite loci with tri- and tetra-nucleotide repeat motifs for Ayu (Plecoglossus altivelis) using next-generation sequencing. Mol Biol Rep 2023; 50:7127-7132. [PMID: 37378743 DOI: 10.1007/s11033-023-08566-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Ayu or sweetfish, Plecoglossus altivelis, an amphidromous fish ranging in the northwestern Pacific, is economically important inland fisheries and aquaculture resources. Genetic characterization of wild Ayu and derived culture seeds with competent molecular genetic markers is still insufficient for their sustainable use. Microsatellite DNA markers with larger repeat motifs (e.g. tri- and tetra-nucleotide motifs) are convenient and accurate compared with those having mono- and di-nucleotide motifs, but the latter motifs characterized most Ayu microsatellite markers developed previously. METHODS AND RESULTS Here, we isolated and characterized 17 polymorphic microsatellite DNA markers with tri- and tetra-nucleotide repeat motif using next-generation sequencing. Alleles per locus varied from 6 to 23. The observed and expected heterozygosities ranged from 0.542 to 1.000 and 0.709 to 0.951, respectively. Polymorphic information content (PIC) of 15 out of the 17 loci were high (≧ 0.700), suggesting them to be highly informative. Twelve of the 17 loci were used for preliminary assignment test among three collections, and successfully allocated the examined fish to the original populations. CONCLUSION The novel polymorphic microsatellite markers developed herein will be useful to examine the genetic diversity and population structure of wild Ayu and the effect of seed transplantation on native populations, providing a tool for conservation and sustainable adaptive management of this species.
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Affiliation(s)
- Hideharu Tsukagoshi
- Sanriku Fisheries Research Center, Iwate University, 3-75-1 Heita, Kamaishi, Iwate, 026-0001, Japan.
| | - Syuiti Abe
- Sanriku Fisheries Research Center, Iwate University, 3-75-1 Heita, Kamaishi, Iwate, 026-0001, Japan
- Graduate School of Fisheries Sciences, Hokkaido University, Minatocho 3-1-1, Hakodate, 041-8611, Japan
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Tran HL, Mai HP, Le Thi D, Thi ND, Le Tung L, Thanh TP, Manh HT, Mau HN, Chu HH, Hoang H. The first maternal genetic study of hunter-gatherers from Vietnam. Mol Genet Genomics 2023:10.1007/s00438-023-02050-0. [PMID: 37438447 DOI: 10.1007/s00438-023-02050-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.
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Affiliation(s)
- Huyen Linh Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Pham Mai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Dung Le Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nhung Doan Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Lam Le Tung
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Tung Pham Thanh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Ha Tran Manh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hung Nguyen Mau
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam.
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Riley R, Mathieson I, Mathieson S. INTERPRETING GENERATIVE ADVERSARIAL NETWORKS TO INFER NATURAL SELECTION FROM GENETIC DATA. bioRxiv 2023:2023.03.07.531546. [PMID: 36945387 PMCID: PMC10028936 DOI: 10.1101/2023.03.07.531546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Understanding natural selection in humans and other species is a major focus for the use of machine learning in population genetics. Existing methods rely on computationally intensive simulated training data. Unlike efficient neutral coalescent simulations for demographic inference, realistic simulations of selection typically requires slow forward simulations. Because there are many possible modes of selection, a high dimensional parameter space must be explored, with no guarantee that the simulated models are close to the real processes. Mismatches between simulated training data and real test data can lead to incorrect inference. Finally, it is difficult to interpret trained neural networks, leading to a lack of understanding about what features contribute to classification. Here we develop a new approach to detect selection that requires relatively few selection simulations during training. We use a Generative Adversarial Network (GAN) trained to simulate realistic neutral data. The resulting GAN consists of a generator (fitted demographic model) and a discriminator (convolutional neural network). For a genomic region, the discriminator predicts whether it is "real" or "fake" in the sense that it could have been simulated by the generator. As the "real" training data includes regions that experienced selection and the generator cannot produce such regions, regions with a high probability of being real are likely to have experienced selection. To further incentivize this behavior, we "fine-tune" the discriminator with a small number of selection simulations. We show that this approach has high power to detect selection in simulations, and that it finds regions under selection identified by state-of-the art population genetic methods in three human populations. Finally, we show how to interpret the trained networks by clustering hidden units of the discriminator based on their correlation patterns with known summary statistics. In summary, our approach is a novel, efficient, and powerful way to use machine learning to detect natural selection.
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Affiliation(s)
- Rebecca Riley
- Department of Computer Science, Haverford College, Haverford PA, 19041 USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, 19104 USA
| | - Sara Mathieson
- Department of Computer Science, Haverford College, Haverford PA, 19041 USA
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Soresinetti L, Arnoldi I, Negri A, Naro G, Michelutti A, Montarsi F, Mosca A, Bandi C, Gabrieli P, Epis S. Development of microsatellite markers for the invasive mosquito Aedes koreicus. Parasit Vectors 2023; 16:223. [PMID: 37415250 PMCID: PMC10324130 DOI: 10.1186/s13071-023-05823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/28/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Aedes koreicus is a mosquito species native to East Asia which has recently invaded several countries in Europe. In Italy, this mosquito was first detected in the North-East in 2011 and is now widely distributed in the entire northern part of the country. The development of specific genetic markers, such as microsatellites, is necessary to uncover the dispersal routes of this mosquito from its native areas and, eventually, to plan future control interventions. METHODS Available raw sequences of genomic DNA of Ae. koreicus were screened in silico using BLASTn to identify possible microsatellite-containing sequences. Specific primer pairs were then designed, and their efficiency was determined through polymerase chain reaction (PCR) on 32 individuals of Ae. koreicus collected in Italy. PCR conditions were optimised in three multiplex reactions. Genotyping of individual mosquitoes was performed on both single and multiplex PCR reactions. Finally, analysis of intra-population variation was performed to assess the level of polymorphism of the markers. RESULTS Mosquito genotyping provided consistent results in both single and multiplex reactions. Out of the 31 microsatellite markers identified in the Ae. koreicus genome raw sequences, 11 were polymorphic in the examined mosquito samples. CONCLUSIONS The results show that the 11 microsatellite markers developed here hold potential for investigating the genetic structure of Ae. koreicus populations. These markers could thus represent a novel and useful tool to infer the routes of invasion of this mosquito species into Europe and other non-native areas.
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Affiliation(s)
- Laura Soresinetti
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Irene Arnoldi
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
- University School of Advanced Studies Pavia, IUSS, 27100 Pavia, Italy
- Italian Malaria Network, Inter University Center for Malaria Research, University of Milan, 20133 Milan, Italy
| | - Agata Negri
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- Italian Malaria Network, Inter University Center for Malaria Research, University of Milan, 20133 Milan, Italy
- Department of Environmental Biology, Sapienza University of Rome, Via Dei Sardi 70, 00185 Rome, Italy
| | - Giovanni Naro
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
| | - Alice Michelutti
- Istituto Zooprofilattico Sperimentale Delle Venezie, 35020 Legnaro, Italy
| | - Fabrizio Montarsi
- Istituto Zooprofilattico Sperimentale Delle Venezie, 35020 Legnaro, Italy
| | - Andrea Mosca
- Istituto Per Le Piante da Legno E L ’Ambiente, I.P.L.A. S.P.A, 10132 Turin, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- University School of Advanced Studies Pavia, IUSS, 27100 Pavia, Italy
- Italian Malaria Network, Inter University Center for Malaria Research, University of Milan, 20133 Milan, Italy
| | - Paolo Gabrieli
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- University School of Advanced Studies Pavia, IUSS, 27100 Pavia, Italy
- Italian Malaria Network, Inter University Center for Malaria Research, University of Milan, 20133 Milan, Italy
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center “Romeo Ed Enrica Invernizzi”, University of Milan, 20133 Milan, Italy
- University School of Advanced Studies Pavia, IUSS, 27100 Pavia, Italy
- Italian Malaria Network, Inter University Center for Malaria Research, University of Milan, 20133 Milan, Italy
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Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. OBJECTIVES To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. METHODS Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. RESULTS Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. CONCLUSION Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Haspel RL, Schneider WH, Vege S, Brunker PAR. Blood Group Serology and "Race": Looking Back to Move Forward. Transfus Med Rev 2023; 37:150749. [PMID: 37827585 DOI: 10.1016/j.tmrv.2023.150749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 10/14/2023]
Abstract
Less than a decade after the discovery of the ABO antigens as a Mendelian inherited trait, blood group antigen frequencies were first used to define racial groups. This approach, known as seroanthropology, was the basis for collecting large amounts of blood group frequency data in different populations and was also sometimes used for racist purposes. Ultimately, population geneticists used these data to disprove race as a biological construct. Through understanding the history of seroanthropology, and recognizing the harms of its lingering presence, healthcare providers can better practice race-conscious, as opposed to race-based, transfusion medicine.
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Affiliation(s)
- Richard L Haspel
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - William H Schneider
- Department of History, Medical Humanities and Health Studies, Indiana University, Indianapolis, IN, USA
| | - Sunitha Vege
- Immunohematology and Genomics, New York Blood Center, New York, NY, USA
| | - Patricia A R Brunker
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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Tan F, Li W, Feng H, Huang Y, Banerjee AK. Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome. PeerJ 2023; 11:e15527. [PMID: 37397021 PMCID: PMC10309054 DOI: 10.7717/peerj.15527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels.
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Affiliation(s)
- Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Weixi Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hui Feng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yelin Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Nunes I, Passos K, Mourão Ximenes A, Hrbek T, Farias IP. Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin. PeerJ 2023; 11:e15503. [PMID: 37361032 PMCID: PMC10289084 DOI: 10.7717/peerj.15503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/14/2023] [Indexed: 06/28/2023] Open
Abstract
Background Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.
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Affiliation(s)
- Ingrid Nunes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Kelmer Passos
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Aline Mourão Ximenes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brasil
| | - Tomas Hrbek
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Department of Biology, Trinity University, San Antonio, TX, United States of America
| | - Izeni Pires Farias
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
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Nzioka A, Madeira MJ, Kokokiris L, Ortiz-Zarrogoitia M, Diaz de Cerio O, Cancio I. Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea. Mar Environ Res 2023; 189:106058. [PMID: 37379782 DOI: 10.1016/j.marenvres.2023.106058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023]
Abstract
Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2-19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (FST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.
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Affiliation(s)
- Anthony Nzioka
- CBET Research Group, Dept. Zoology & Animal Cell Biology, Faculty of Science & Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza Hiribidea s/n, 48620, Plentzia, Basque Country, Spain
| | - María José Madeira
- SystBioGen Research Group, Dept. Zoology & Animal Cell Biology, Faculty of Science & Technology and Lucio Lascaray Research Centre, University of the Basque Country, Calle Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Lambros Kokokiris
- Department of Nutritional Sciences & Dietetics, International Hellenic University, P.O. 141 Sindos, 57400, Thessaloniki, Greece
| | - Maren Ortiz-Zarrogoitia
- CBET Research Group, Dept. Zoology & Animal Cell Biology, Faculty of Science & Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza Hiribidea s/n, 48620, Plentzia, Basque Country, Spain
| | - Oihane Diaz de Cerio
- CBET Research Group, Dept. Zoology & Animal Cell Biology, Faculty of Science & Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza Hiribidea s/n, 48620, Plentzia, Basque Country, Spain
| | - Ibon Cancio
- CBET Research Group, Dept. Zoology & Animal Cell Biology, Faculty of Science & Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza Hiribidea s/n, 48620, Plentzia, Basque Country, Spain.
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Wade CM, Nuttall R, Liu S. Comprehensive analysis of geographic and breed-purpose influences on genetic diversity and inherited disease risk in the Doberman dog breed. Canine Med Genet 2023; 10:7. [PMID: 37277858 DOI: 10.1186/s40575-023-00130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Publicly available phenotype data and genotyping array data from two citizen science projects: "Doberman Health Surveys" and "The Doberman Diversity Project" were analyzed to explore relative homozygosity, diversity, and disorder risk according to geographical locale and breeding purpose in the Doberman. RESULTS From the phenotypic data cohort, life expectancy of a Doberman at birth is 9.1 years. The leading causes of death were heart disease (accounting for 28% of deaths) and cancers (collectively accounting for 14% of deaths). By genotyping, the world Doberman population exists as four major cohorts (European exhibition-bred, Americas exhibition-bred, European work, Americas pet/informal). Considering the entire Doberman population, four genomic regions longer than 500 Kb are fixed in 90% or more of 3,226 dogs included in this study. The four fixed regions reside on two autosomal chromosomes: CFA3:0.8-2.3 Mb (1.55 Mb); CFA3: 57.9-59.8 Mb (1.8 Mb); CFA31:0-1.2 Mb (1.2 Mb); and CFA31:4.80-6.47 Mb (1.67 Mb). Using public variant call files including variants for eight Doberman pinschers, we observed 30 potentially functional alternate variants that were evolutionarily diverged relative to the wider sequenced dog population within the four strongly homozygous chromosomal regions. Effective population size (Ne) is a statistical measure of breed diversity at the time of sampling that approximates the number of unique individuals. The major identified sub-populations of Dobermans demonstrated Ne in the range 70-236. The mean level of inbreeding in the Doberman breed is 40% as calculated by the number of array variants in runs of homozygosity divided by the assayed genome size (excluding the X chromosome). The lowest observed level of inbreeding in the Dobermans assayed was 15% in animals that were first generation mixes of European and USA bred Dobermans. Array variant analysis shows that inter-crossing between European and USA-bred Dobermans has capacity to re-introduce variation at many loci that are strongly homozygous. CONCLUSIONS We conclude that efforts to improve breed diversity first should focus on regions with the highest fixation levels, but managers must ensure that mutation loads are not worsened by increasing the frequencies of rarer haplotypes in the identified regions. The analysis of global data identified regions of strong fixation that might impact known disorder risks in the breed. Plausible gene candidates for future analysis of the genetic basis of cardiac disease and cancer were identified in the analysis.
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Affiliation(s)
- Claire M Wade
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.
| | | | - Sophie Liu
- Doberman Diversity Project, Oakland, CA, USA
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Filoglu G, Duvenci A, Tas S, Karadayi H, Asicioglu F, Bulbul O. Development of a multiplex panel with 36 insertion/deletion markers (InDel) for individual identification. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00652-z. [PMID: 37266863 DOI: 10.1007/s12024-023-00652-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/03/2023]
Abstract
In recent years, the insertion/deletion (InDel) polymorphism has become a preferred genetic marker in forensic genetics due to its low mutation rates and small amplicon sizes. In this study, a 36-InDelplex identification panel, consisting of autosomal 34 InDel loci, 1 Y InDel locus, and amelogenin, was developed, and gene frequencies in the Turkish population were determined. The loci of the InDel panel with global minimum allele frequencies (MAF) ≥ 0.4 were selected from the 1000 Genomes Project Phase 3 data. The amplicon sizes of the loci were designed in the range of 69-252 bp. In the validation study of the developed panel, analysis threshold, dynamic range, sensitivity, stochastic threshold, inhibitor tolerance, and reproducibility parameters were studied by following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The sensitivity studies indicated that complete and reliable InDel profiles could be obtained with 0.25 ng of DNA. A population study was evaluated using 250 samples from Turkey. The mean observed heterozygosity ratio (Ho) of all loci was 0.48. The combined discrimination power (CPD) is 0.999999999990867 and the combined exclusion probability (CPE) was 0.9930. The population comparison was also made using Turkish and the five major populations from the 1000 Genomes Phase 3 populations' data (Africa, Europe, East Asia, South Asia, and America). In conclusion, the results showed that the 36-InDelplex panel is a reliable, sensitive, and accurate system that is suitable for human identification and population genetics purposes.
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Affiliation(s)
- Gonul Filoglu
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey
| | - Arzu Duvenci
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey
| | - Sebahat Tas
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey
| | - Huseyin Karadayi
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey
| | - Faruk Asicioglu
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science and Legal Medicine, Istanbul University- Cerrahpasa, 34500, Istanbul, Turkey.
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Chen S, Duan L, Li S, Zhou J, Zhou Y, Yang Y, Liu M, Wang Y, Xia S, Xu J, Lü S. [Preliminary study on the mechanism underlying the ecological isolation of Oncomelania hupensis populations in Changde City]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2023; 35:147-154. [PMID: 37253563 DOI: 10.16250/j.32.1374.2022276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To investigate ecological isolation between Oncomelania hupensis snail populations in hilly regions and marshland and lake regions in Yuanjiang valley, Changde City, Hunan Province, and to unravel its underlying mechanisms. METHODS Taoyuan County, Shimen County, Linli County and Lixian County in Changde City were selected as snail sampling sites in hilly regions, and Lixian County, Jinshi City, West Lake Administration District, Hanshou County and Dingcheng District were selected as snail sampling sites in marshland and lake areas. Cytochrome C oxidase 1 (cox 1) gene was amplified in snail samples and sequenced. The genetic sequences of O. hupensis snails were aligned using the software MEGA 11, and the haplotypes of O. hupensis snails were determined using the software DNASP 5.10.01. The phylogenetic tree was generated using Bayesian inference with the software MrBayes 3.2, and analysis of molecular variance (AMOVA) was performed to analyze the source of genetic divergence and estimate the genetic divergence index (FST) among snail populations with the software Arlequin 3.5.2.2. The genetic barrier among 11 O. hupensis snail populations was estimated using the Monmonier algorithm of adegenet toolkit in R package. The settings with "land in winter and water in summer" in the Yuanjian River section were divided into two categories according to the upstream and downstream, and the areas with "land in winter and water in summer" in the upstream and downstream were transformed into raster data, and then loaded into the software Fragstats 4 for analysis of landscape indicators. The trends in changes of digital elevation were extracted from the Yuanjiang River section based on the digital elevation model, and made three-dimensional visualization using the R package. RESULTS The mitochondrial cox 1 gene were amplified in 165 O. hupensis snais from 11 sampling sites and sequenced, and a total of 152 valid gene sequences were obtained, with 46 haplotypes or 9 populations determined. No haplotype was shared in snails between Taoyuan County and Dingcheng District and Hanshou County along the downstream of the Yuanjiang River. The total area of settings with "land in winter and water in summer" was 617.66 hm2 in the upsteram of the Yuanjiang River, which consisted of 473 patches, with each patch measuring 1.31 hm2, the largest area index of 0.735 2, the landscape division index of 0.999 9, and the landscape shape index of 45.293 7. The total area of settings with "land in winter and water in summer" was 9 956.92 hm2 in the downstream of the Yuanjiang River, which consisted of 771 patches, with each patch measuring 12.91 hm2, the largest area index of 97.839 9, the landscape division index of 0.042 7, and the landscape shape index of 7.249 6. The area of settings with "land in winter and water in summer" was much larger in the downstream than that in the upstream of the Yuanjiang River, and the stronger landscape connectivity and non-remarkable alteration of riverbed elevation provided suitable habitats for snail breeding. CONCLUSIONS The hydrological and environmental characteristics of the upstream of the Yuanjiang River restrain the breeding and spread of O. hupensis, resulting in ecological isolation between Oncomelania hupensis in Taoyuan County and those in the downstream of Yuanjiang River.
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Affiliation(s)
- S Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of National Health Commission on Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
| | - L Duan
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of National Health Commission on Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
| | - S Li
- Hunan Institute of Schistosomiasis Control, China
| | - J Zhou
- Hunan Institute of Schistosomiasis Control, China
| | - Y Zhou
- Changde Center for Disease Control and Prevention, Hunan Province, China
| | - Y Yang
- Health Bureau of Taoyuan County, Changde City, Hunan Province, China
| | - M Liu
- Health Bureau of Hanshou County, Hunan Province, China
| | - Y Wang
- Health Department of Dingcheng District, Changde City, Hunan Province, China
| | - S Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of National Health Commission on Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - J Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of National Health Commission on Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
| | - S Lü
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of National Health Commission on Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Nemati H, Kaveh K, Ejtehadi MR. Counterintuitive properties of evolutionary measures: A stochastic process study in cyclic population structures with periodic environments. J Theor Biol 2023; 564:111436. [PMID: 36828246 DOI: 10.1016/j.jtbi.2023.111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/24/2023]
Abstract
Local environmental interactions are a major factor in determining the success of a new mutant in structured populations. Spatial variations in the concentration of genotype-specific resources change the fitness of competing strategies locally and thus can drastically change the outcome of evolutionary processes in unintuitive ways. The question is how such local environmental variations in network population structures change the condition for selection and fixation probability of an advantageous (or deleterious) mutant. We consider linear graph structures and focus on the case where resources have a spatial periodic pattern. This is the simplest model with two parameters, length scale and fitness scales, representing heterogeneity. We calculate fixation probability and fixation times for a constant population birth-death process as fitness heterogeneity and period vary. Fixation probability is affected by not only the level of fitness heterogeneity but also spatial scale of resources variations set by period of distribution T. We identify conditions for which a previously a deleterious mutant (in a uniform environment) becomes beneficial as fitness heterogeneity is increased. We observe cases where the fixation probability of both mutant and resident types are more than their neutral value, 1/N, simultaneously. This coincides with exponential increase in time to fixation which points to potential coexistence of resident and mutant types. Finally, we discuss the effect of the 'fitness shift' where the fitness function of two types has a phase difference. We observe significant increases (or decreases) in the fixation probability of the mutant as a result of such phase shift.
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Affiliation(s)
- Hossein Nemati
- Sharif University of Technology, Physics Department, Iran
| | - Kamran Kaveh
- University of Washington, Department of Applied Mathematics, United States of America.
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Zang F, Ma Y, Wu Q, Tu X, Xie X, Huang P, Tong B, Zheng Y, Zang D. Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways. BMC Plant Biol 2023; 23:235. [PMID: 37142995 PMCID: PMC10158352 DOI: 10.1186/s12870-023-04244-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions. RESULTS A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth. CONCLUSIONS The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.
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Affiliation(s)
- Fengqi Zang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Yan Ma
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Qichao Wu
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Center for excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan, 650204, P. R. China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China.
| | - Dekui Zang
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China.
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Hirano T, Saito T, Ito S, Ye B, Linscott TM, Do VT, Dong Z, Chiba S. Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia. Mol Phylogenet Evol 2023; 182:107728. [PMID: 36804427 DOI: 10.1016/j.ympev.2023.107728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.
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Affiliation(s)
- Takahiro Hirano
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan.
| | - Takumi Saito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Shun Ito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - T Mason Linscott
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Zhengzhong Dong
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
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84
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Cai J, Zhan J, Arking DE, Bader JS. Priors, population sizes, and power in genome-wide hypothesis tests. BMC Bioinformatics 2023; 24:170. [PMID: 37101120 PMCID: PMC10134629 DOI: 10.1186/s12859-023-05261-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNAseq data, carry a high multiple testing burden. This burden can be overcome by enrolling larger cohorts or alleviated by using prior biological knowledge to favor some hypotheses over others. Here we compare these two methods in terms of their abilities to boost the power of hypothesis testing. RESULTS We provide a quantitative estimate for progress in cohort sizes and present a theoretical analysis of the power of oracular hard priors: priors that select a subset of hypotheses for testing, with an oracular guarantee that all true positives are within the tested subset. This theory demonstrates that for GWAS, strong priors that limit testing to 100-1000 genes provide less power than typical annual 20-40% increases in cohort sizes. Furthermore, non-oracular priors that exclude even a small fraction of true positives from the tested set can perform worse than not using a prior at all. CONCLUSION Our results provide a theoretical explanation for the continued dominance of simple, unbiased univariate hypothesis tests for GWAS: if a statistical question can be answered by larger cohort sizes, it should be answered by larger cohort sizes rather than by more complicated biased methods involving priors. We suggest that priors are better suited for non-statistical aspects of biology, such as pathway structure and causality, that are not yet easily captured by standard hypothesis tests.
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Affiliation(s)
- Jitong Cai
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jianan Zhan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Dan E Arking
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.
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85
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Guo F, Liu Z, Long G, Zhang B, Dong X, Liu D, Yu S. High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System. Forensic Sci Int Genet 2023; 65:102879. [PMID: 37150076 DOI: 10.1016/j.fsigen.2023.102879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.
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Affiliation(s)
- Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Xinyu Dong
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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86
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Mei S, Yi S, Cai M, Zhang Y, Cui W, Xu H, Lan Q, Zhu B. Exploring the forensic effectiveness and population genetic differentiation by self-constructed 41 multi-InDel panel in Yunnan Zhuang group. Gene 2023; 860:147180. [PMID: 36669579 DOI: 10.1016/j.gene.2023.147180] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Yunnan is one of the main residences of the Zhuang group which is one of the 55 ethnic minorities in China. At present, there are relatively few researches on population genetics and forensic science of the Yunnan Zhuang group. Therefore, this study used a self-constructed panel containing 41 multi-InDel markers to analyze the genetic polymorphisms of 173 individuals from Yunnan Zhuang group. The results indicated that these 41 multi-InDels in Yunnan Zhuang group were highly polymorphic markers expect for three markers. The cumulative match probability and combined exclusion probability values of the 40 multi-InDels (MI38 marker was excluded) were 8.0671E-26 and 0.9999995959, respectively. In addition, population genetic analyses were performed on genotyping data of 41 multi-InDel markers among the Yunnan Zhuang and 26 reference populations, revealing that the Yunnan Zhuang group was genetically close to the five populations in East Asia. According to the STRUCTURE analysis, the Yunnan Zhuang group presented similar ancestral compositions to the five populations from East Asia, and when the K value was three, the five intercontinental populations showed their different genetic structures. In conclusion, the 41 multi-InDel markers could be used as an effective tool for individual identification and paternity testing of the Zhuang group in Yunnan province, as well as for their ancestry information inference studies.
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Affiliation(s)
- Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital; Southern Medical University, Guangzhou 510515, China.
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87
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Hernández-Lozano MY, Cruz-Barraza JA, Rocha-Olivares A. Isolation and characterization of novel microsatellite loci for the Eastern Pacific marine sponge Mycale cecilia by Illumina MiSeq sequencing. Mol Biol Rep 2023; 50:5489-5493. [PMID: 37031324 DOI: 10.1007/s11033-023-08320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 02/02/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND Mycale cecilia is an abundant Eastern Tropical Pacific sponge living in a wide variety of habitats, including coral reefs where it may directly interact with corals. It is also known to possess secondary metabolites of pharmacological value. These aspects highlight the importance of having a better understanding of its biology, and genetic and population diversity. METHODS AND RESULTS In the present study, we isolated and characterized twelve novel microsatellite loci by Illumina MiSeq sequencing. The loci were tested in 30 specimens collected from two coral reef localities (La Paz, Baja California Sur and Isabel Island, Nayarit) from the Mexican Pacific using M13(-21) labeling. All loci were polymorphic, with two to nine alleles per locus. Expected heterozygosities varied from 0.616 to 0.901. Eleven loci were tested and successfully amplified in M. microsigmatosa from the Gulf of Mexico. CONCLUSION Here we report the first microsatellite loci developed for a sponge species from the Eastern Pacific coast. These molecular markers will be used for population genetic studies of M. cecilia, and potentially in other congeneric species; particularly in vulnerable marine areas that require protection, such as coral reefs.
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Affiliation(s)
- Misha Yazmín Hernández-Lozano
- Posgrado en Ciencias del Mar y Limnología, UNAM, Mazatlán, México
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Unidad Académica de Mazatlán, Av. Joel Montes Camarena s/n, Mazatlán, Sinaloa, 82000, CP, México
| | - José Antonio Cruz-Barraza
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Unidad Académica de Mazatlán, Av. Joel Montes Camarena s/n, Mazatlán, Sinaloa, 82000, CP, México.
| | - Axayácatl Rocha-Olivares
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
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88
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Abstract
Comparative studies of hominids have long sought to identify mutational events that shaped the evolution of the human nervous system. However, functional genetic differences are outnumbered by millions of nearly neutral mutations, and the developmental mechanisms underlying human nervous system specializations are difficult to model and incompletely understood. Candidate-gene studies have attempted to map select human-specific genetic differences to neurodevelopmental functions, but it remains unclear how to contextualize the relative effects of genes that are investigated independently. Considering these limitations, we discuss scalable approaches for probing the functional contributions of human-specific genetic differences. We propose that a systems-level view will enable a more quantitative and integrative understanding of the genetic, molecular and cellular underpinnings of human nervous system evolution.
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Affiliation(s)
- Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/@TylerFair_
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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89
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Mussmann SM, Harrison AS, Wilson WD. Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis. Mol Biol Rep 2023. [PMID: 36939964 DOI: 10.1007/s11033-023-08376-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023]
Abstract
BACKGROUND Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes. METHODS AND RESULTS Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (P. o. sonoriensis). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests. CONCLUSIONS This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other Poeciliopsis species of Mexico and Central America.
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90
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Zhou X, Wang L, Zhu P, Yang Z, Wang Z, Chen Y, Gu X, He R, Xu J, Jing B, Yang G, Chen S, Wu S, Xie Y. Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens. Parasit Vectors 2023; 16:109. [PMID: 36935516 PMCID: PMC10026407 DOI: 10.1186/s13071-023-05712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria is one of the most severe chicken diseases and poses a great economic threat to the poultry industry. Understanding the evolutionary biology of chicken Eimeria parasites underpins development of new interactions toward the improved prevention and control of this poultry disease. METHODS We presented an evolutionary blueprint of chicken coccidia by genetically characterizing complete mitogenome assemblies of 33 isolates representing all seven known Eimeria species infecting chickens in China. Further genome- and gene-level phylogenies were also achieved to better understand the evolutionary relationships of these chicken Eimeria at the species level. RESULTS 33 mitogenomes of chicken eimerian parasites ranged from 6148 bp to 6480 bp in size and encoded typical mitochondrial compositions of apicomplexan parasites including three protein-coding genes (PCGs), seven fragmented small subunit (SSU) and 12/13 fragmented large subunit (LSU) rRNAs. Comparative genomics provided an evolutionary scenario for the genetic diversity of PCGs-cytochrome c oxidase subunits 1 and 3 (cox1 and cox3) and cytochrome b (cytb); all were under purifying selection with cox1 and cox3 being the lowest and highest evolutionary rates, respectively. Genome-wide phylogenies classified the 33 Eimeria isolates into seven subgroups, and furthermore Eimeria tenella and Eimeria necatrix were determined to be more closely related to each other than to the other eight congenic species. Single/concatenated mitochondrial protein gene-based phylogenies supported cox1 as the genetic marker for evolutionary and phylogenetic studies for avain coccidia. CONCLUSIONS To our knowledge, these are the first population-level mitogenomic data on the genus Eimeria, and its comprehensive molecular characterization provides valuable resources for systematic, population genetic and evolutionary biological studies of apicomplexan parasites in poultry.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Zijiang Yang
- Tokyo University of Marine Science and Technology, Konan Minato-Ku, Tokyo, 1088477, Japan
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Yijun Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
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Thorn CS, Maness RW, Hulke JM, Delmore KE, Criscione CD. Population genomics of helminth parasites. J Helminthol 2023; 97:e29. [PMID: 36927601 DOI: 10.1017/s0022149x23000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.
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Affiliation(s)
- C S Thorn
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - R W Maness
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - J M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - K E Delmore
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - C D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
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92
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Das S, Máquina M, Phillips K, Cuamba N, Marrenjo D, Saúte F, Paaijmans KP, Huijben S. Fine-scale spatial distribution of deltamethrin resistance and population structure of Anopheles funestus and Anopheles arabiensis populations in Southern Mozambique. Malar J 2023; 22:94. [PMID: 36915131 PMCID: PMC10010967 DOI: 10.1186/s12936-023-04522-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Insecticide resistance in malaria vectors can be spatially highly heterogeneous, yet population structure analyses frequently find relatively high levels of gene flow among mosquito populations. Few studies have contemporaneously assessed phenotypic, genotypic and population structure analysis on mosquito populations and none at fine geographical scales. In this study, genetic diversity, population structure, and insecticide resistance profiles of Anopheles funestus and Anopheles arabiensis were examined across mosquito populations from and within neighbouring villages. METHODS Mosquitoes were collected from 11 towns in southern Mozambique, as well as from different neighbourhoods within the town of Palmeira, during the peak malaria transmission season in 2016. CDC bottle bioassay and PCR assays were performed with Anopheles mosquitoes at each site to determine phenotypic and molecular insecticide resistance profiles, respectively. Microsatellite analysis was conducted on a subsample of mosquitoes to estimate genetic diversity and population structure. RESULTS Phenotypic insecticide resistance to deltamethrin was observed in An. funestus sensu stricto (s.s.) throughout the area, though a high level of mortality variation was seen. However, 98% of An. funestus s.s. were CYP6P9a homozygous resistant. An. arabiensis was phenotypically susceptible to deltamethrin and 99% were kdr homozygous susceptible. Both Anopheles species exhibited high allelic richness and heterozygosity. Significant deviations from Hardy-Weinberg equilibrium were observed, and high linkage disequilibrium was seen for An. funestus s.s., supporting population subdivision. However, the FST values were low for both anophelines (- 0.00457 to 0.04213), Nm values were high (9.4-71.8 migrants per generation), AMOVA results showed almost 100% genetic variation among and within individuals, and Structure analysis showed no clustering of An. funestus s.s. and An. arabiensis populations. These results suggest high gene flow among mosquito populations. CONCLUSION Despite a relatively high level of phenotypic variation in the An. funestus population, molecular analysis shows the population is admixed. These data indicate that CYP6P9a resistance markers do not capture all phenotypic variation in the area, but also that resistance genes of high impact are likely to easily spread in the area. Conversely, other strategies, such as transgenic mosquito release programmes will likely not face challenges in this locality.
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Affiliation(s)
- Smita Das
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.,PATH, Seattle, WA, USA
| | - Mara Máquina
- Centro de Investigação em Saúde de Manhiça (CISM), Fundação Manhiça, Manhica, Mozambique
| | - Keeley Phillips
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Nelson Cuamba
- Programa Nacional de Controlo da Malária, Ministério da Saúde, Maputo, Mozambique.,PMI VectorLink Project, Abt Associates Inc., Maputo, Mozambique
| | - Dulcisaria Marrenjo
- Programa Nacional de Controlo da Malária, Ministério da Saúde, Maputo, Mozambique
| | - Francisco Saúte
- Centro de Investigação em Saúde de Manhiça (CISM), Fundação Manhiça, Manhica, Mozambique
| | - Krijn P Paaijmans
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA.,The Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA.,ISGlobal, Barcelona, Spain
| | - Silvie Huijben
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA. .,Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA.
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Sibly RM, Curnow RN. Allele frequencies and selection coefficients in locally adapted populations. J Theor Biol 2023; 565:111463. [PMID: 36914112 DOI: 10.1016/j.jtbi.2023.111463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/15/2023]
Abstract
Understanding the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting at the genetic level in the wild. This is challenging to achieve but may be easier in the case of populations in migration-selection balance. When two populations are at equilibrium under migration-selection balance, there exist loci whose alleles are selected different ways in the two populations. Such loci can be identified from genome sequencing by their high values of FST. This raises the question of what is the strength of selection on locally-adaptive alleles. To answer this question we analyse a 1-locus 2-allele model of a population distributed between two niches. We show by simulation of selected cases that the outputs from finite-population models are essentially the same as those from deterministic infinite-population models. We then derive theory for the infinite-population model showing the dependence of selection coefficients on equilibrium allele frequencies, migration rates, dominance and relative population sizes in the two niches. An Excel spreadsheet is provided for the calculation of selection coefficients and their approximate standard errors from observed values of population parameters. We illustrate our results with a worked example, with graphs showing the dependence of selection coefficients on equilibrium allele frequencies, and graphs showing how FST depends on the selection coefficients acting on the alleles at a locus. Given the extent of recent progress in ecological genomics, we hope our methods may help those studying migration-selection balance to quantify the advantages conferred by adaptive genes.
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Affiliation(s)
| | - Robert N Curnow
- Department of Mathematics and Statistics, University of Reading, UK.
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94
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Du Q, Ma G, Lu C, Wang Q, Fu L, Cong B, Li S. Development and evaluation of a novel panel containing 188 microhaplotypes for 2nd-degree kinship testing in the Hebei Han population. Forensic Sci Int Genet 2023; 65:102855. [PMID: 36947934 DOI: 10.1016/j.fsigen.2023.102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Distant kinship identification is one of the critical problems in forensic genetics. As a new type of genetic marker defined and discussed in the last decade, the microhaplotype (MH) has drawn much attention in such identification owing to its specific advantages to traditional short tandem repeat (STR) or single nucleotide polymorphism (SNP) markers. In this study, MH markers were screened step by step from the 1000 Genomes Project database, and a novel multiplex panel containing 188 MHs (in which 181 are reported the first time, while 1 was reported in a previous study and the other 6 have partial overlaps with known markers) was constructed for application in 2nd- and 3rd-degree kinship identification. Along with the construction, a novel MH nomenclature was proposed, in which the SNP position information they contained was taken into account to eliminate the possibility that the same locus was named differently interlaboratory. After a series of evaluations, the panel was shown to have good sequencing accuracy, high sensitivity, species specificity, and resistance to anti-PCR inhibitors or degradation. Population data of the 188 MHs were calculated based on the genetic information of 221 unrelated Hebei Han individuals, and the effective number of alleles (Ae) ranged from 2.0925 to 8.2634 (with an average of 2.9267). For the whole system, the cumulative matching probability (CMP), the cumulative power of exclusion in paternity testing of duos (CPEduo) and that of trios (CPEtrio) reached 2.8422 × 10-137, 1-1.3109 × 10-21, and 1-2.8975 × 10-39, respectively, indicating that this panel was satisfactory for individual identification and paternity testing. Then, the efficiency of the 188 MHs in 2nd- and 3rd-degree kinship testing was studied based on 30 extended families consisting of 179 2nd-degree and 121 3rd-degree relatives, as well as simulations of 0.5 million pairs of those two kinships. The results showed that clear opinions would be given in 83.36% of 2nd-degree identifications with a false rate less than 10-5, when the confirming and excluding thresholds of cumulative likelihood ratio (CLR) were set as 104 and 10-4, respectively. This panel is still not sufficient to solve the problem of 3rd-degree kinship identification alone, and approximately 300 or 870 MH loci would be needed in 2nd- or 3rd-degree kinship identification, respectively, to achieve a system efficiency not less than 0.99 with such a threshold set; such necessary numbers would be used only as a reference in further research.
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Affiliation(s)
- Qingqing Du
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Guanju Ma
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Chaolong Lu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Qian Wang
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Lihong Fu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Shujin Li
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China.
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95
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Dai X, Zhu Q, Wang C, Rukeye A, Cao Z, Shan T, Wang Y, Zhang J. F ST estimates of 94 populations in China based on STR markers. Forensic Sci Int Genet 2023; 64:102854. [PMID: 36893618 DOI: 10.1016/j.fsigen.2023.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the FST values. Thus, FST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific FST values of each population, the overall FST values of each province, each region, and the whole country, and the locus-specific FST values of different loci were calculated. The LRs using different allele frequencies and different FST values were compared based on the combination of simulated genotypes. As a result, the FST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after FST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding FST values can make the LRs more accurate and reasonable.
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Affiliation(s)
- Xuan Dai
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Zhu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Chu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Aosiman Rukeye
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Ze Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Tiantian Shan
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yufang Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
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96
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Shaikevich E, Karan L, Fedorova M. Genetic Structure of Aedes ( Stegomyia) albopictus Populations in Russia. J Arthropod Borne Dis 2023; 17:51-62. [PMID: 37609565 PMCID: PMC10440497 DOI: 10.18502/jad.v17i1.13201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2023] [Indexed: 08/24/2023] Open
Abstract
Background Aedes (Stegomyia) albopictus was found for the first time in 2011 on the Black Sea coast in Russia, and during 2011-2019, the species expanded over two climate zones Cfa and Csa. Methods Here, we studied the sequence diversity of the mitochondrial cytochrome c oxidase I (COI) gene, 1317-1433bp in length. In total, 131 specimens of Ae. albopictus sampled from 21 locations in Russia and Abkhazia were examined. Results Two of the six identified mitochondrial haplotypes were detected for the first time. Four COI haplotypes were shared by at least two studied local populations. The most prevalent H1 and H2 haplotypes dominated in all the sampled localities in the Cfa zone. The H3 haplotype was prevalent in the Csa zone. Other haplotypes were rare. Phylogenetic analyses, spatial isolation and limited gene flow revealed that the samples from the Csa zone differed significantly from those from the Cfa zone. Conclusion Two spatially isolated genetic lineages exist in Ae. albopictus population in southern region of Russia. One lineage obtained on the seacoast and inland (in valleys of the Caucasus Mountains and steppe zone) is widely distributed worldwide including Mediterranean populations. This confirms the hypothesis that the emergence of Ae. albopictus population in southern region of Russia may be associated with the terrestrial spread of mosquitoes from the well-established European population due to human activity. The other lineage, discovered in Novorossiysk, a maritime port, is similar to Ae. albopictus from the USA and Japan, suggesting the independent introduction of these mosquitoes.
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Affiliation(s)
- Elena Shaikevich
- Vavilov Institute of General Genetics, Gubkin str. 3, 119333 Moscow, Russia
| | - Ludmila Karan
- Central Research Institute of Epidemiology, Novogireevskaya str., 3a, 111123 Moscow, Russia
| | - Marina Fedorova
- Central Research Institute of Epidemiology, Novogireevskaya str., 3a, 111123 Moscow, Russia
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97
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Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. Immunoinformatics (Amst) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
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Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
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98
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Mullett MS, Van Poucke K, Haegeman A, Focquet F, Cauldron NC, Knaus BJ, Horta Jung M, Kageyama K, Hieno A, Masuja H, Uematsu S, Webber JF, Brasier CM, Bakonyi J, Heungens K, Grünwald NJ, Jung T. Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora. IMA Fungus 2023; 14:4. [PMID: 36823663 DOI: 10.1186/s43008-023-00109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.
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99
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Alvarado-Sizzo H, Alcántara-Ayala O, Espinosa D, Rivas G, Oyama K, Luna-Vega I. Genomic-based microsatellite development for Ternstroemia (Pentaphylacaceae) and transferability to other Ericales. Mol Biol Rep 2023. [PMID: 36787057 DOI: 10.1007/s11033-023-08258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach. METHODS AND RESULTS We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3-14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales. CONCLUSIONS These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications.
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100
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Ibrahim A, Manko E, Dombrowski JG, Campos M, Benavente ED, Nolder D, Sutherland CJ, Nosten F, Fernandez D, Vélez-Tobón G, Castaño AT, Aguiar ACC, Pereira DB, da Silva Santos S, Suarez-Mutis M, Di Santi SM, Regina de Souza Baptista A, Dantas Machado RL, Marinho CR, Clark TG, Campino S. Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. Lancet Reg Health Am 2023; 18:100420. [PMID: 36844008 PMCID: PMC9950661 DOI: 10.1016/j.lana.2022.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 01/03/2023]
Abstract
Background Brazil is a unique and understudied setting for malaria, with complex foci of transmission associated with human and environmental conditions. An understanding of the population genomic diversity of P. vivax parasites across Brazil can support malaria control strategies. Methods Through whole genome sequencing of P. vivax isolates across 7 Brazilian states, we use population genomic approaches to compare genetic diversity within country (n = 123), continent (6 countries, n = 315) and globally (26 countries, n = 885). Findings We confirm that South American isolates are distinct, have more ancestral populations than the other global regions, with differentiating mutations in genes under selective pressure linked to antimalarial drugs (pvmdr1, pvdhfr-ts) and mosquito vectors (pvcrmp3, pvP45/48, pvP47). We demonstrate Brazil as a distinct parasite population, with signals of selection including ABC transporter (PvABCI3) and PHIST exported proteins. Interpretation Brazil has a complex population structure, with evidence of P. simium infections and Amazonian parasites separating into multiple clusters. Overall, our work provides the first Brazil-wide analysis of P. vivax population structure and identifies important mutations, which can inform future research and control measures. Funding AI is funded by an MRC LiD PhD studentship. TGC is funded by the Medical Research Council (Grant no. MR/M01360X/1, MR/N010469/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1). SC is funded by Medical Research Council UK grants (MR/M01360X/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1) and Bloomsbury SET (ref. CCF17-7779). FN is funded by The Shloklo Malaria Research Unit - part of the Mahidol Oxford Research Unit, supported by the Wellcome Trust (Grant no. 220211). ARSB is funded by São Paulo Research Foundation - FAPESP (Grant no. 2002/09546-1). RLDM is funded by Brazilian National Council for Scientific and Technological Development - CNPq (Grant no. 302353/2003-8 and 471605/2011-5); CRFM is funded by FAPESP (Grant no. 2020/06747-4) and CNPq (Grant no. 302917/2019-5 and 408636/2018-1); JGD is funded by FAPESP fellowships (2016/13465-0 and 2019/12068-5) and CNPq (Grant no. 409216/2018-6).
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Affiliation(s)
- Amy Ibrahim
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Mónica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Colin J. Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak,
Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of
Clinical Medicine Research Building, University of Oxford Old Road Campus,
Oxford, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | - Gabriel Vélez-Tobón
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | | | | | | | - Simone da Silva Santos
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | - Martha Suarez-Mutis
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | | | - Andrea Regina de Souza Baptista
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Ricardo Luiz Dantas Machado
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Claudio R.F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Taane G. Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Faculty of Epidemiology & Population Health, London School of Hygiene
& Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
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