1
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Beaumont R, Akam L, Singh P, Bhatti JS, Mastana S. Genomic diversity and differentiation of Alu insertion polymorphisms in a native British and four South Asian migrant populations. Ann Hum Biol 2023; 50:117-122. [PMID: 36786492 DOI: 10.1080/03014460.2023.2180091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
BACKGROUND Alu insertions are bi-allelic and primate-specific, this makes them a useful marker for studying genetic variation, migration patterns, forensic analyses, paternity, and evolutionary heritage; however, specific population studies are limited. AIM The objective of this study is to document the level and extent of genetic variation at 39 different Alu loci in five populations (British, Indian Punjabi, Indian Gujarati, Pakistani, and Bangladeshi) from the East Midlands region of the UK. Genetic data on migrant populations is currently limited. SUBJECTS AND METHODS DNA samples (n = 543) were analysed for 39 Alu insertion polymorphisms using specific primers and standard protocols. Data were analysed for population and forensic genetic parameters. RESULTS All studied Alus were polymorphic in the British White population while South Asian migrant populations had a variable number of loci which were monomorphic. Highest heterozygosities and lowest match probabilities were observed in the British sample, while the Bangladeshi sample had the lowest heterozygosity and higher match probability. CONCLUSION The analysed Alus insertions (TPA25, Ya5NBC123, Ya5NBC182, Ya5NBC241, and Ya5NBC242) are highly polymorphic and variable among migrant populations. These loci could be useful for population genomic and differentiation studies.
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Affiliation(s)
- Rebekah Beaumont
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Liz Akam
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Sarabjit Mastana
- Human Genomics Lab, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
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2
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Balachandran P, Walawalkar IA, Flores JI, Dayton JN, Audano PA, Beck CR. Transposable element-mediated rearrangements are prevalent in human genomes. Nat Commun 2022; 13:7115. [PMID: 36402840 PMCID: PMC9675761 DOI: 10.1038/s41467-022-34810-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.
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Affiliation(s)
| | | | - Jacob I Flores
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jacob N Dayton
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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3
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Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. NAR Genom Bioinform 2022; 4:lqac009. [PMID: 35178516 PMCID: PMC8846365 DOI: 10.1093/nargab/lqac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.
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Affiliation(s)
- P Prakrithi
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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4
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Voicu AA, Krützen M, Bilgin Sonay T. Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution. FRONTIERS IN BIOINFORMATICS 2021; 1:695784. [PMID: 36303734 PMCID: PMC9581056 DOI: 10.3389/fbinf.2021.695784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.
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Affiliation(s)
| | - Michael Krützen
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Tugce Bilgin Sonay
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
- *Correspondence: Tugce Bilgin Sonay,
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5
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Abeid SN, Motrane M, Farhane H, Harich N. Human population genetics of Comoros islanders: Alu polymorphisms and the peopling of the three major islands. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Zhang C, Xiao X, Li T, Li M. Translational genomics and beyond in bipolar disorder. Mol Psychiatry 2021; 26:186-202. [PMID: 32424235 DOI: 10.1038/s41380-020-0782-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWAS) have revealed multiple genomic loci conferring risk of bipolar disorder (BD), providing hints for its underlying pathobiology. However, there are still remaining questions to answer. For example, discordance exists between BD heritability estimated with earlier epidemiological evidence and that calculated based on common GWAS variations. Where is the "missing heritability"? How can we explain the biology of the disease based on genetic findings? In this review, we summarize the accomplishments and limitations of current BD GWAS, and discuss potential reasons for the "missing heritability." In addition, progresses of research for the biological mechanisms underlying BD genetic risk using brain tissues, reprogrammed cells, and model animals are reviewed. While our knowledge of BD genetic basis is significantly promoted by these efforts, the complexities of gene regulation in the genome, the spatial-temporal heterogeneity during brain development, and the limitations of different experimental models should always be considered. Notably, several genes have been widely studied given their relatively well-characterized involvement in BD (e.g., CACAN1C and ANK3), and findings of these genes are summarized to both outline possible biological mechanisms of BD and describe examples of translating GWAS discoveries into the pathophysiology.
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Affiliation(s)
- Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tao Li
- Mental Health Center and Psychiatric Laboratory, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China. .,West China Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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7
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Liu W, Li W, Cai X, Yang Z, Li H, Su X, Song M, Zhou DS, Li X, Zhang C, Shao M, Zhang L, Yang Y, Zhang Y, Zhao J, Chang H, Yao YG, Fang Y, Lv L, Li M, Xiao X. Identification of a functional human-unique 351-bp Alu insertion polymorphism associated with major depressive disorder in the 1p31.1 GWAS risk loci. Neuropsychopharmacology 2020; 45:1196-1206. [PMID: 32193514 PMCID: PMC7235090 DOI: 10.1038/s41386-020-0659-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/16/2020] [Accepted: 03/11/2020] [Indexed: 12/28/2022]
Abstract
Genome-wide association studies (GWAS) have reported substantial single-nucleotide polymorphisms (SNPs) associated with major depressive disorder (MDD), but the underlying functional variations in the GWAS risk loci are unclear. Here we show that the European MDD genome-wide risk-associated allele of rs12129573 at 1p31.1 is associated with MDD in Han Chinese, and this SNP is in strong linkage disequilibrium (LD) with a human-unique Alu insertion polymorphism (rs70959274) in the 5' flanking region of a long non-coding RNA (lncRNA) LINC01360 (Long Intergenic Non-Protein Coding RNA 1360), which is preferably expressed in human testis in the currently available expression datasets. The risk allele at rs12129573 is almost completely linked with the absence of this Alu insertion. The Alu insertion polymorphism (rs70959274) is significantly associated with a lower RNA level of LINC01360 and acts as a transcription silencer likely through modulating the methylation of its internal CpG sites. Luciferase assays confirm that the presence of Alu insertion at rs70959274 suppresses transcriptional activities in human cells, and deletion of the Alu insertion through CRISPR/Cas9-directed genome editing increases RNA expression of LINC01360. Deletion of the Alu insertion in human cells also leads to dysregulation of gene expression, biological processes and pathways relevant to MDD, such as the alterations of mRNA levels of DRD2 and FLOT1, transcription of genes involved in synaptic transmission, neurogenesis, learning or memory, and the PI3K-Akt signaling pathway. In summary, we identify a human-unique DNA repetitive polymorphism in robust LD with the MDD risk-associated SNP at the prominent 1p31.1 GWAS loci, and offer insights into the molecular basis of the illness.
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Affiliation(s)
- Weipeng Liu
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Wenqiang Li
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Xin Cai
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Zhihui Yang
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Huijuan Li
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Xi Su
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Meng Song
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Dong-Sheng Zhou
- 0000 0004 1782 599Xgrid.452715.0Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Xingxing Li
- 0000 0004 1782 599Xgrid.452715.0Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Chen Zhang
- 0000 0004 0368 8293grid.16821.3cShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minglong Shao
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Luwen Zhang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Yongfeng Yang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Yan Zhang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Jingyuan Zhao
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Hong Chang
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yong-Gang Yao
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China ,0000000119573309grid.9227.eCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China ,0000000119573309grid.9227.eKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yiru Fang
- 0000 0004 0368 8293grid.16821.3cShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,0000000119573309grid.9227.eCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Province People's Hospital, Zhengzhou, Henan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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8
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Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ, Konkel MK, Batzer MA. Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. Mob DNA 2019; 10:46. [PMID: 31788036 PMCID: PMC6880559 DOI: 10.1186/s13100-019-0187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Background Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput "poly-Detect" method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.
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Affiliation(s)
- Jerilyn A Walker
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Vallmer E Jordan
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Jessica M Storer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Cody J Steely
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Paulina Gonzalez-Quiroga
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Thomas O Beckstrom
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Lydia C Rewerts
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Corey P St Romain
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Catherine E Rockwell
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Jeffrey Rogers
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Clifford J Jolly
- 4Department of Anthropology, New York University, New York, NY 10003 USA
| | - Miriam K Konkel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA.,Department of Genetics & Biochemistry, Clemson Center for Human Genetics, Clemson, SC 29634 USA
| | | | - Mark A Batzer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
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9
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Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
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10
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Kshatriya GK, Panmei T, Kameih G. Alu insertion-deletion polymorphisms in the Tibeto-Burman speaking tribal groups of Manipur, North-East India. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Doronina L, Reising O, Clawson H, Ray DA, Schmitz J. True Homoplasy of Retrotransposon Insertions in Primates. Syst Biol 2019; 68:482-493. [PMID: 30445649 DOI: 10.1093/sysbio/syy076] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 01/24/2023] Open
Abstract
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human-chimpanzee-rhesus macaque) and 0.02-0.04% (for human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable. [Homoplasy; precise deletions; precise parallel insertions; primates; retrotransposons.].
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Olga Reising
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, TX, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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12
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Badache H, Boussetta S, Elgaaeid AB, Cherni L, El-khil HK. Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers. Ann Hum Biol 2019; 46:150-159. [DOI: 10.1080/03014460.2019.1588994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hocine Badache
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Amel Benammar Elgaaeid
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
| | - Houssein Khodjet El-khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
- Department of Biomedical Sciences, College of Health Sciences Qatar University, Doha, Qatar
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13
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Singh G, Sandhu HS, Sharma R, Srinivas Y, Matharoo K, Singh M, Bhanwer AJS. Genetic variation and population structure of five ethnic groups from Punjab, North-West India: Analysis of MHC class I polymorphic Alu insertions (POALINs). Gene 2019; 701:173-178. [PMID: 30935920 DOI: 10.1016/j.gene.2019.03.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 01/31/2023]
Abstract
Genetic variation and differentiation of five ethnic groups from Punjab, North-West India was characterized by analyzing data on polymorphic Alu insertions (POALINs) within the class I genomic region of major histocompatibility complex (MHC), which is completely non-existent in Indian population. The haplotype frequency, distribution and heterozygosity among these groups and their potential implications in molecular anthropology and evolutionary studies were also determined. A total of 479 unrelated healthy individuals representing five different ethnic groups: Banias, Brahmins, Khatri, Jat Sikhs and Scheduled Castes were genotyped for five MHC Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) using polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. No significant deviation from Hardy-Weinberg equilibrium was observed, except for the AluHJ locus in Brahmins. The POALINs varied in allele frequency between 0.0260 and 0.4427. The average heterozygosity among the studied groups ranged from 0.1937 in Banias to 0.2666 in Jat Sikhs. The genetic differentiation among the studied groups was observed to be of the order of 0.01302. Single POALIN haplotypes were found to be more frequent than multiple POALIN haplotypes. The results of inter-population differentiations, haplotype frequencies, genetic distances, multidimensional scaling, phylogenetic and structure analyses indicated close genetic relationships between the five ethnic groups of Punjab, North-West India. Analyses of polymorphic Alu loci of MHC genomic region may represent reliable information about the ancestry, demographic history and geographic origins of the various human populations, facilitating better understanding of the evolutionary, forensic and epidemiological prospective.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh 160014, India; Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Harkirat Singh Sandhu
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, NY 10029, USA
| | - Rubina Sharma
- Department of Surgery-Transplant, Regenerative Medicine, DRC-II, University of Nebraska Medical Center, Omaha, NE 68198-5965, USA
| | | | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Manroop Singh
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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14
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Moshiri N, Mirarab S. A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. Syst Biol 2018; 67:475-489. [PMID: 29165679 DOI: 10.1093/sysbio/syx088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 11/15/2017] [Indexed: 11/14/2022] Open
Abstract
Models of tree evolution have mostly focused on capturing the cladogenesis processes behind speciation. Processes that derive the evolution of genomic elements, such as repeats, are not necessarily captured by these existing models. In this article, we design a model of tree evolution that we call the dual-birth model, and we show how it can be useful in studying the evolution of short Alu repeats found in the human genome in abundance. The dual-birth model extends the traditional birth-only model to have two rates of propagation, one for active nodes that propagate often, and another for inactive nodes, that with a lower rate, activate and start propagating. Adjusting the ratio of the rates controls the expected tree balance. We present several theoretical results under the dual-birth model, introduce parameter estimation techniques, and study the properties of the model in simulations. We then use the dual-birth model to estimate the number of active Alu elements and their rates of propagation and activation in the human genome based on a large phylogenetic tree that we build from close to one million Alu sequences.
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Affiliation(s)
- Niema Moshiri
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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15
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Di Santo Meztler GP, Del Palacio S, Esteban ME, Armoa I, Argüelles CF, Catanesi CI. Genetic Differentiation of North-East Argentina Populations Based on 30 Binary X Chromosome Markers. Front Genet 2018; 9:208. [PMID: 29951085 PMCID: PMC6008373 DOI: 10.3389/fgene.2018.00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/24/2018] [Indexed: 01/21/2023] Open
Abstract
Alu insertions, INDELs, and SNPs in the X chromosome can be useful not only for revealing relationships among populations but also for identification purposes. We present data of 10 Alu insertions, 5 INDELs, and 15 SNPs of X-chromosome from three Argentinian north-east cities in order to gain insight into the genetic diversity of the X chromosome within this region of the country. Data from 198 unrelated individuals belonging to Posadas, Corrientes, and Eldorado cities were genotyped for Ya5DP62, Yb8DP49, Ya5DP3, Ya5NBC37, Ya5DP77, Ya5NBC491, Ya5DP4, Ya5DP13, Yb8NBC634, and Yb8NBC102 Alu insertions, for MID193, MID1705, MID3754, MID3756 and MID1540 Indels and for rs6639398, rs5986751, rs5964206, rs9781645, rs2209420, rs1299087, rs318173, rs933315, rs1991961, rs4825889, rs1781116, rs1937193, rs1781104, rs149910, and rs652 SNPs. No deviations from Hardy-Weinberg equilibrium were observed for Posadas and Corrientes. However, Eldorado showed significant values, and it was found to have an internal substructuring with two groups of different origin, one showing higher similarity with European countries, and the other with more similarities to Posadas and Corrientes. Fst pairwise genetic distances emerged for some markers among the studied populations and also between our data and those from other countries and continents. Of particular interest, Alu insertions demonstrated the most differences, and could be of use in ancestry studies for these populations, while INDELs and SNPs variation were informative for differentiation within the country.
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Affiliation(s)
- Gabriela P Di Santo Meztler
- Laboratorio de Diversidad Genética, IMBICE, CICPBA-Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Santiago Del Palacio
- Instituto Argentino de Radioastronomía, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, CICPBA, Villa Elisa, Argentina
| | - María E Esteban
- Secció de Zoologia i Antropologia Biológica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Isaías Armoa
- Dirección de Desarrollo e Integración Regional Municipalidad de Eldorado, Misiones, Argentina
| | - Carina F Argüelles
- LACyGH-GIGA, Instituto de Biología Subtropical, nodo Posadas-Dpto. de Genética-FCEQyN UNaM-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina
| | - Cecilia I Catanesi
- Laboratorio de Diversidad Genética, IMBICE, CICPBA-Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.,Cátedra de Genética, Facultad de Cs. Naturales y Museo, UNLP, La Plata, Argentina
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16
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Gray JM, Orlans HO, Shanks M, Clouston P, MacLaren RE. Slowly progressive retinitis pigmentosa caused by two novel mutations in the MAK gene. Ophthalmic Genet 2018; 39:508-511. [PMID: 29781741 DOI: 10.1080/13816810.2018.1474369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND The growing number of clinical trials currently underway for inherited retinal diseases has highlighted the importance of achieving a molecular diagnosis for all new cases presenting to hospital eye services. The male germ cell-associated kinase (MAK) gene encodes a cilium-associated protein selectively expressed in the retina and testis, and has recently been implicated in autosomal recessive retinitis pigmentosa (RP). Whole exome sequencing has previously identified a homozygous Alu insertion in probands with recessive RP and nonsense and missense mutations have also been reported. MATERIALS AND METHODS Here we describe two novel mutations in different alleles of the MAK gene in a 75-year-old British female, who had a clinical diagnosis of RP () with onset in the fourth decade and no relevant family history. The mutations were established through next generation sequencing of a panel of 111 genes associated with RP and RP-like phenotypes. RESULTS Two novel null mutations were identified within the MAK gene. The first c.1195_1196delAC p.(Thr399fs), was a two base-pair deletion creating a frame-shift in exon 9 predicted to result in nonsense-mediated decay. The second, c.279-2A>G, involved the splice acceptor consensus site upstream of exon 4, predicted to lead to aberrant splicing. CONCLUSIONS The natural history of this individual's RP is consistent with previously described MAK mutations, being significantly milder than that associated with other photoreceptor ciliopathies. We suggest inclusion of MAK as part of wider genetic testing in all individuals presenting with RP.
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Affiliation(s)
- Joanna Monika Gray
- a Nuffield Laboratory of Ophthalmology & Oxford Biomedical Research Centre , University of Oxford , Oxford , UK.,b Oxford Eye Hospital , John Radcliffe Hospital , Oxford , UK
| | - Harry Otway Orlans
- a Nuffield Laboratory of Ophthalmology & Oxford Biomedical Research Centre , University of Oxford , Oxford , UK.,b Oxford Eye Hospital , John Radcliffe Hospital , Oxford , UK
| | - Morag Shanks
- c Oxford Medical Genetics Laboratories , Oxford University Hospitals NHS Foundation Trust , Oxford , UK
| | - Penny Clouston
- c Oxford Medical Genetics Laboratories , Oxford University Hospitals NHS Foundation Trust , Oxford , UK
| | - Robert Elvis MacLaren
- a Nuffield Laboratory of Ophthalmology & Oxford Biomedical Research Centre , University of Oxford , Oxford , UK.,b Oxford Eye Hospital , John Radcliffe Hospital , Oxford , UK
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17
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Jordan VE, Walker JA, Beckstrom TO, Steely CJ, McDaniel CL, St Romain CP, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mob DNA 2018; 9:13. [PMID: 29632618 PMCID: PMC5885306 DOI: 10.1186/s13100-018-0118-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio, the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of Alu insertion polymorphisms unique to the Papio lineage. To complete these analyses, we created a computational algorithm to identify novel Alu insertions in next-generation sequencing data. Results We identified 187,379 Alu insertions present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve Papio baboons: two from each of the six extant Papio species. These data were used to construct a whole genome Alu-based phylogeny of Papio baboons. The resulting cladogram fully-resolved relationships within Papio. Conclusions These data represent the most comprehensive Alu-based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved Alu-based phylogeny of Papio baboons. Electronic supplementary material The online version of this article (10.1186/s13100-018-0118-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vallmer E Jordan
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Jerilyn A Walker
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Thomas O Beckstrom
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Cody J Steely
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Cullen L McDaniel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | - Corey P St Romain
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
| | | | - Kim C Worley
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jane Phillips-Conroy
- 4Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clifford J Jolly
- 5Department of Anthropology, New York University, New York, NY 10003 USA
| | - Jeffrey Rogers
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Miriam K Konkel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA.,6Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Mark A Batzer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803 USA
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18
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Steely CJ, Baker JN, Walker JA, Loupe CD, Batzer MA. Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. Mob DNA 2018; 9:10. [PMID: 29560044 PMCID: PMC5858127 DOI: 10.1186/s13100-018-0115-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.
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Affiliation(s)
- Cody J Steely
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Jasmine N Baker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Charles D Loupe
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
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19
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Baker JN, Walker JA, Denham MW, Loupe CD, Batzer MA. Recently integrated Alu insertions in the squirrel monkey ( Saimiri) lineage and application for population analyses. Mob DNA 2018; 9:9. [PMID: 29449901 PMCID: PMC5808450 DOI: 10.1186/s13100-018-0114-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups. RESULTS PCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382 Alu insertion events ≤2% diverged from 46 different Alu subfamily consensus sequences, 25 Saimiri specific and 21 NWM specific Alu subfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 different Saimiri specific Alu subfamilies and 75 elements from 19 different NWM specific Alu subfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110 Alu insertion polymorphisms, 51 had species informative allele frequency distributions between Saimiri sciureus and Saimiri boliviensis groups. CONCLUSIONS This study confirms the evolution of Alu subfamilies in Saimiri and provides evidence for an ongoing and prolific expansion of these elements in Saimiri with many active subfamilies concurrently propagating. The subset of polymorphic Alu insertions with species informative allele frequency distribution between Saimiri sciureus and Saimiri boliviensis will be instructive for specimen identification and conservation biology.
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Affiliation(s)
- Jasmine N. Baker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Michael W. Denham
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Charles D. Loupe
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
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20
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Nyirenda MJ. Non-communicable diseases in sub-Saharan Africa: understanding the drivers of the epidemic to inform intervention strategies. Int Health 2017; 8:157-8. [PMID: 27178673 DOI: 10.1093/inthealth/ihw021] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 11/13/2022] Open
Abstract
Sub-Saharan Africa is experiencing a rapidly increasing epidemic of non-communicable diseases (NCDs), while it continues to face longstanding challenges from infectious diseases. This double burden of disease could have a devastating impact on a continent that already has significant resource constraints, emphasizing the urgent need for appropriate interventions in the region. However, it is crucial to have a careful understanding of the local drivers of NCDs. This should not only include study of the traditional lifestyle risk factors, but also an examination of emerging risk factors (such as the influence of insults early in life or interactions with infection), which may be of particular importance in Africa.
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Affiliation(s)
- Moffat J Nyirenda
- London School of Hygiene & Tropical Medicine, Department of Non-Communicable Disease Epidemiology, Keppel Street, London, WC1E 7HT, UK
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21
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Panjaliya RK, Dogra V, Kumar P, Gupta S. Human-specificAluInsertion/Deletion Polymorphisms in Various Population Groups of Jammu Region. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2012.11886185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rakesh Kumar Panjaliya
- Institute of Human Genetics, University of Jammu, Jammu 180006, Jammu and Kashmir, India
| | - Vikas Dogra
- Institute of Human Genetics, University of Jammu, Jammu 180006, Jammu and Kashmir, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu 180006, Jammu and Kashmir, India
| | - Subash Gupta
- Institute of Human Genetics, University of Jammu, Jammu 180006, Jammu and Kashmir, India
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22
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Walker JA, Jordan VE, Steely CJ, Beckstrom TO, McDaniel CL, St. Romain CP, Bennett EC, Robichaux A, Clement BN, Konkel MK, Batzer MA. Papio Baboon Species Indicative Alu Elements. Genome Biol Evol 2017; 9:1788-1796. [PMID: 28854642 PMCID: PMC5569700 DOI: 10.1093/gbe/evx130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2017] [Indexed: 11/25/2022] Open
Abstract
The genus of Papio (baboon) has six recognized species separated into Northern and Southern clades, each comprised of three species distributed across the African continent. Geographic origin and phenotypic variants such as coat color and body size have commonly been used to identify different species. The existence of multiple hybrid zones, both ancient and current, have complicated efforts to characterize the phylogeny of Papio baboons. More recently, mitochondrial DNA (mtDNA) and Y-chromosome genetic markers have been utilized for species identification with particular focus on the hybrid zones. Alu elements accumulate in a random manner and are a novel source of identical by descent variation with known ancestral states for inferring population genetic and phylogenetic relationships. As part of the Baboon Genome Analysis Consortium, we assembled an Alu insertion polymorphism database of nearly 500 Papio-lineage specific insertions representing all six species and performed population structure and phylogenetic analyses. In this study, we have selected a subset of 48 species indicative Alu insertions and demonstrate their utility as genetic systems for the identification of baboon species within Papio. Individual elements from the panel are easy to genotype and can be used in a hierarchical fashion based on the original level of uncertainty. This Alu-48 panel should serve as a valuable tool during the maintenance of pedigree records in captive populations and assist in the forensic identification of fossils and potential hybrids in the wild.
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Affiliation(s)
| | | | - Cody J. Steely
- Department of Biological Sciences, Louisiana State University
| | | | | | | | | | - Arianna Robichaux
- Department of Biological Sciences, Louisiana State University
- Department of Biological and Physical Sciences, Northwestern State University of Louisiana
| | - Brooke N. Clement
- Department of Biological Sciences, Louisiana State University
- School of Veterinary Medicine, Louisiana State University
| | | | | | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University
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Singh G, Talwar I, Sandhu HS, Matharoo K, Bhanwer AJS. Genetic dissection of five ethnic groups from Punjab, North-West India-A study based on Autosomal Markers. Leg Med (Tokyo) 2017; 26:25-32. [PMID: 28549544 DOI: 10.1016/j.legalmed.2017.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/07/2017] [Accepted: 02/27/2017] [Indexed: 10/20/2022]
Abstract
The present study assessed the applicability of Alu insertion elements and Single Nucleotide Polymorphisms (SNPs) in forensic identification and estimated the extent of genetic variation in five major ethnic groups of Punjab, North-West India. A total of 1012 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris and Scheduled Castes were genotyped for four Alu elements (ACE, APO, PLAT, D1) and six Single Nucleotide Polymorphisms [ESR (PvuII), LPL (PvuII), HTR2A (MspI), DRD2 Taq1A, Taq1B, Taq1D]. Allele frequencies observed heterozygosity and forensic efficacy parameters were determined. The data on the genetic affinity of the studied populations among themselves and with other populations of India was also analysed using a Neighbor-Joining tree and multidimensional scaling plot respectively. All the 10 loci were polymorphic and their average observed heterozygosity ranged from 0.3872 (Banias) to 0.4311 (Scheduled Castes). Allele frequency variation at the 9 out of 10 loci led to statistically significant pairwise differences among the five study population groups. The result from AMOVA, Structure analysis, and Phylogenetic tree suggests that these populations are homogenous. In the multidimensional scaling plot, the present study populations formed a compact cluster clearly separated from other populations, suggesting a unique genetic identity of the Punjab populations as a whole. All these observations suggest that either a recent common origin of these populations or extensive gene flow across the populations that dissolve the original genetic differences. The data generated in this study will be useful for forensic genetics, molecular anthropological and demographic studies.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh 160014, India; Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Indu Talwar
- Department of Anthropology, Panjab University, Chandigarh 160014, India.
| | - Harkirat Singh Sandhu
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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Mastana SS, Bhatti JS, Singh P, Wiles A, Holland J. Genetic variation of MHC Class I polymorphic Alu insertions (POALINs) in three sub-populations of the East Midlands, UK. Ann Hum Biol 2017; 44:562-567. [PMID: 28277746 DOI: 10.1080/03014460.2017.1302507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Alu elements are highly researched due to their useful nature as markers in the study of human population genetics. Recently discovered Major Histocompatibility Complex (MHC) polymorphic Alu insertions (POALINs) have not been examined extensively for genetic variation and their HLA associations. AIMS The aim of this study is to assess the genetic variation between three populations using five recently discovered POALINs. METHODS AND SUBJECTS The study examined 190 healthy, unrelated subjects from three different populations in the East Midlands (UK) for the presence or absence of five Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) via the polymerase chain reaction followed by gel electrophoresis. Data were analysed for genetic variation and phylogenetic analyses. RESULTS All Alus were polymorphic in study populations. Appreciable allele frequency variation was observed at a number of loci. The British population was significantly different from both the Punjabi Jat Sikh and Gujarati Patel populations, although showing a closer genetic relationship to the Punjabi Jat Sikh population than the Gujarati Patel population (Nei's DA = 0.0031 and 0.0064, respectively). CONCLUSIONS MHC POALINs are useful markers in the investigation of genetic variation and the assessment of population relationships, and may have some bearing on disease associations due to their linkage disequilibrium with HLA loci; this warrants further studies.
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Affiliation(s)
- Sarabjit S Mastana
- a Human Genomics Lab , School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
| | - Jasvinder S Bhatti
- b Department of Biotechnology and Bioinformatics , Sri Guru Gobind Singh College, Sector 26 , Chandigarh , India
| | - Puneetpal Singh
- c Department of Human Genetics , Punjabi University , Patiala , Punjab , India
| | - Adam Wiles
- a Human Genomics Lab , School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
| | - Jonathan Holland
- a Human Genomics Lab , School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
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Chinniah R, Vijayan M, Thirunavukkarasu M, Mani D, Raju K, Ravi PM, Sivanadham R, C K, N M, Karuppiah B. Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India. PLoS One 2016; 11:e0157468. [PMID: 27315142 PMCID: PMC4912101 DOI: 10.1371/journal.pone.0157468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/31/2016] [Indexed: 11/18/2022] Open
Abstract
Seven human-specific Alu markers were studied in 574 unrelated individuals from 10 endogamous groups and 2 hill tribes of Tamil Nadu and Kerala states. DNA was isolated, amplified by PCR-SSP, and subjected to agarose gel electrophoresis, and genotypes were assigned for various Alu loci. Average heterozygosity among caste populations was in the range of 0.292-0.468. Among tribes, the average heterozygosity was higher for Paliyan (0.3759) than for Kani (0.2915). Frequency differences were prominent in all loci studied except Alu CD4. For Alu CD4, the frequency was 0.0363 in Yadavas, a traditional pastoral and herd maintaining population, and 0.2439 in Narikuravars, a nomadic gypsy population. The overall genetic difference (Gst) of 12 populations (castes and tribes) studied was 3.6%, which corresponds to the Gst values of 3.6% recorded earlier for Western Asian populations. Thus, our study confirms the genetic similarities between West Asian populations and South Indian castes and tribes and supported the large scale coastal migrations from Africa into India through West Asia. However, the average genetic difference (Gst) of Kani and Paliyan tribes with other South Indian tribes studied earlier was 8.3%. The average Gst of combined South and North Indian Tribes (CSNIT) was 9.5%. Neighbor joining tree constructed showed close proximity of Kani and Paliyan tribal groups to the other two South Indian tribes, Toda and Irula of Nilgiri hills studied earlier. Further, the analysis revealed the affinities among populations and confirmed the presence of North and South India specific lineages. Our findings have documented the highly diverse (micro differentiated) nature of South Indian tribes, predominantly due to isolation, than the endogamous population groups of South India. Thus, our study firmly established the genetic relationship of South Indian castes and tribes and supported the proposed large scale ancestral migrations from Africa, particularly into South India through West Asian corridor.
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Affiliation(s)
- Rathika Chinniah
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
| | - Murali Vijayan
- Department of Biotechnology & Genetic Engineering, School of Biotechnology, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Manikandan Thirunavukkarasu
- Department of Biotechnology & Genetic Engineering, School of Biotechnology, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - Dhivakar Mani
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
| | - Kamaraj Raju
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
| | - Padma Malini Ravi
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
| | - Ramgopal Sivanadham
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
| | - Kandeepan C
- Department of Zoology, A.P.A.College of Arts & Culture, Palani, 624 601, Tamil Nadu, India
| | - Mahalakshmi N
- Regional Forensic Science Laboratory, Madurai, 625 020, Tamil Nadu, India
| | - Balakrishnan Karuppiah
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, Tamil Nadu, India
- * E-mail:
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Paramasivam R, Reangasamy N, Arumugam D, Krishnan P. Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.56431/p-044q85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure (BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0). Specifically, the DD genotype is more evident among the females (OR = 0 .705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.
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Paramasivam R, Rengasamy N, Arumugam D, Krishnan P. Association of ACE DD Genotype with Hypertension among the Tribal Populations of South India. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.18052/www.scipress.com/ilns.52.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure (BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0). Specifically, the DD genotype is more evident among the females (OR = 0 .705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.
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Abstract
Background The human genome contains several active families of transposable elements (TE): Alu, L1 and SVA. Germline transposition of these elements can lead to polymorphic TE (polyTE) loci that differ between individuals with respect to the presence/absence of TE insertions. Limited sets of such polyTE loci have proven to be useful as markers of ancestry in human population genetic studies, but until this time it has not been possible to analyze the full genomic complement of TE polymorphisms in this way. Results For the first time here, we have performed a human population genetic analysis based on a genome-wide polyTE data set consisting of 16,192 loci genotyped in 2,504 individuals across 26 human populations. PolyTEs are found at very low frequencies, > 93 % of loci show < 5 % allele frequency, consistent with the deleteriousness of TE insertions. Nevertheless, polyTEs do show substantial geographic differentiation, with numerous group-specific polymorphic insertions. African populations have the highest numbers of polyTEs and show the highest levels of polyTE genetic diversity; Alu is the most numerous and the most diverse polyTE family. PolyTE genotypes were used to compute allele sharing distances between individuals and to relate them within and between human populations. Populations and continental groups show high coherence based on individuals’ polyTE genotypes, and human evolutionary relationships revealed by these genotypes are consistent with those seen for SNP-based genetic distances. The patterns of genetic diversity encoded by TE polymorphisms recapitulate broad patterns of human evolution and migration over the last 60–100,000 years. The utility of polyTEs as ancestry informative markers is further underscored by their ability to accurately predict both ancestry and admixture at the continental level. A genome-wide list of polyTE loci, along with their population group-specific allele frequencies and FST values, is provided as a resource for investigators who wish to develop panels of TE-based ancestry markers. Conclusions The genetic diversity represented by TE polymorphisms reflects known patterns of human evolution, and ensembles of polyTE loci are suitable for both ancestry and admixture analyses. The patterns of polyTE allelic diversity suggest the possibility that there may be a connection between TE-based genetic divergence and population-specific phenotypic differences. ᅟ ![]()
Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0052-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230 USA ; PanAmerican Bioinformatics Institute, Cali, Valle del Cauca Colombia ; BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas Colombia
| | - Carlos E Tellez Villa
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca Colombia ; Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230 USA ; PanAmerican Bioinformatics Institute, Cali, Valle del Cauca Colombia ; BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas Colombia
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Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
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SANTOVITO ALFREDO, CERVELLA PIERO, DELPERO MASSIMILIANO. Alu insertion polymorphisms in four ethnic groups from northern Ivory Coast. ANTHROPOL SCI 2014. [DOI: 10.1537/ase.131107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- ALFREDO SANTOVITO
- University of Turin, Department of Life Sciences and Systems Biology, Torino
| | - PIERO CERVELLA
- University of Turin, Department of Life Sciences and Systems Biology, Torino
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Veracx A, Boutellis A, Raoult D. Genetic recombination events between sympatric Clade A and Clade C lice in Africa. JOURNAL OF MEDICAL ENTOMOLOGY 2013; 50:1165-1168. [PMID: 24180123 DOI: 10.1603/me13028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Human head and body lice have been classified into three phylogenetic clades (Clades A, B, and C) based on mitochondrial DNA. Based on nuclear markers (the 18S rRNA gene and the PM2 spacer), two genotypes of Clade A head and body lice, including one that is specifically African (Clade A2), have been described. In this study, we sequenced the PM2 spacer of Clade C head lice from Ethiopia and compared these sequences with sequences from previous works. Trees were drawn, and an analysis of genetic diversity based on the cytochrome b gene and the PM2 spacer was performed for African and non-African lice. In the tree drawn based on the PM2 spacer, the African and non-African lice formed separate clusters. However, Clade C lice from Ethiopia were placed within the African Clade A subcluster (Clade A2). This result suggests that recombination events have occurred between Clade A2 lice and Clade C lice, reflecting the sympatric nature of African lice. Finally, the PM2 spacer and cytochrome b gene sequences of human lice revealed a higher level of genetic diversity in Africa than in other regions.
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Affiliation(s)
- Aurélie Veracx
- Aix Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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Abstract
We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.
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Kumari V, Iyer LR, Roy R, Bhargava V, Panda S, Paul J, Verweij JJ, Clark CG, Bhattacharya A, Bhattacharya S. Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping. BMC Genomics 2013; 14:432. [PMID: 23815468 PMCID: PMC3716655 DOI: 10.1186/1471-2164-14-432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/20/2013] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histolytica isolates are more virulent than others, suggesting that virulence may be linked to genotype. Here we have looked at the genomic distribution of the retrotransposable short interspersed nuclear elements EhSINE1 and EhSINE2. Due to their mobile nature, some EhSINE copies may occupy different genomic locations among isolates of E. histolytica possibly affecting adjacent gene expression; this variability in location can be exploited to differentiate strains. RESULTS We have looked for EhSINE1- and EhSINE2-occupied loci in the genome sequence of Entamoeba histolytica HM-1:IMSS and searched for homologous loci in other strains to determine the insertion status of these elements. A total of 393 EhSINE1 and 119 EhSINE2 loci were analyzed in the available sequenced strains (Rahman, DS4-868, HM1:CA, KU48, KU50, KU27 and MS96-3382. Seventeen loci (13 EhSINE1 and 4 EhSINE2) were identified where a EhSINE1/EhSINE2 sequence was missing from the corresponding locus of other strains. Most of these loci were unoccupied in more than one strain. Some of the loci were analyzed experimentally for SINE occupancy using DNA from strain Rahman. These data helped to correctly assemble the nucleotide sequence at three loci in Rahman. SINE occupancy was also checked at these three loci in 7 other axenically cultivated E. histolytica strains and 16 clinical isolates. Each locus gave a single, specific amplicon with the primer sets used, making this a suitable method for strain typing. Based on presence/absence of SINE and amplification with locus-specific primers, the 23 strains could be divided into eleven genotypes. The results obtained by our method correlated with the data from other typing methods. We also report a bioinformatic analysis of EhSINE2 copies. CONCLUSIONS Our results reveal several loci with extensive polymorphism of SINE occupancy among different strains of E. histolytica and prove the principle that the genomic distribution of SINEs is a valid method for typing of E. histolytica strains.
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Affiliation(s)
- Vandana Kumari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Lakshmi Rani Iyer
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Riti Roy
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Varsha Bhargava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suchita Panda
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Jaco J Verweij
- Laboratory for Medical Microbiology and Immunology, Laboratory for Clinical Pathology, St. Elisabeth Hospital, Tilburg, The Netherlands
| | - C Graham Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Teixeira-Silva A, Silva RM, Carneiro J, Amorim A, Azevedo L. The role of recombination in the origin and evolution of Alu subfamilies. PLoS One 2013; 8:e64884. [PMID: 23750218 PMCID: PMC3672193 DOI: 10.1371/journal.pone.0064884] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/19/2013] [Indexed: 01/25/2023] Open
Abstract
Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.
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Affiliation(s)
- Ana Teixeira-Silva
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Raquel M. Silva
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - João Carneiro
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - António Amorim
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Luísa Azevedo
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- * E-mail:
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Distribution of beta-globin haplotypes among the tribes of southern Gujarat, India. Gene 2013; 521:287-92. [DOI: 10.1016/j.gene.2013.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/13/2012] [Accepted: 02/27/2013] [Indexed: 11/17/2022]
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Wang K, Li Y, Dai C, Wang K, Yu J, Tan Y, Zhang W, Yu XF. Characterization of the relationship between APOBEC3B deletion and ACE Alu insertion. PLoS One 2013; 8:e64809. [PMID: 23717661 PMCID: PMC3663847 DOI: 10.1371/journal.pone.0064809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/18/2013] [Indexed: 12/15/2022] Open
Abstract
The insertion/deletion (I/D) polymorphism of the angiotensin converting enzyme (ACE), commonly associated with many diseases, is believed to have affected human adaptation to environmental changes during the out-of-Africa expansion. APOBEC3B (A3B), a member of the cytidine deaminase family APOBEC3s, also exhibits a variable gene insertion/deletion polymorphism across world populations. Using data available from published reports, we examined the global geographic distribution of ACE and A3B genotypes. In tracking the modern human dispersal routes of these two genes, we found that the variation trends of the two I/D polymorphisms were directly correlated. We observed that the frequencies of ACE insertion and A3B deletion rose in parallel along the expansion route. To investigate the presence of a correlation between the two polymorphisms and the effect of their interaction on human health, we analyzed 1199 unrelated Chinese adults to determine their genotypes and other important clinical characteristics. We discovered a significant difference between the ACE genotype/allele distribution in the A3B DD and A3B II/ID groups (P = 0.045 and 0.015, respectively), indicating that the ACE Alu I allele frequency in the former group was higher than in the latter group. No specific clinical phenotype could be associated with the interaction between the ACE and A3B I/D polymorphisms. A3B has been identified as a powerful inhibitor of Alu retrotransposition, and primate A3 genes have undergone strong positive selection (and expansion) for restricting the mobility of endogenous retrotransposons during evolution. Based on these findings, we suggest that the ACE Alu insertion was enabled (facilitated) by the A3B deletion and that functional loss of A3B provided an opportunity for enhanced human adaptability and survival in response to the environmental and climate challenges arising during the migration from Africa.
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Affiliation(s)
- Kang Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yuanyuan Li
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chunyan Dai
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Kaishi Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Jinghua Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yiran Tan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Xiao-Fang Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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Pugach I, Delfin F, Gunnarsdóttir E, Kayser M, Stoneking M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proc Natl Acad Sci U S A 2013; 110:1803-8. [PMID: 23319617 PMCID: PMC3562786 DOI: 10.1073/pnas.1211927110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Dridi S. Alu mobile elements: from junk DNA to genomic gems. SCIENTIFICA 2012; 2012:545328. [PMID: 24278713 PMCID: PMC3820591 DOI: 10.6064/2012/545328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/06/2012] [Indexed: 06/02/2023]
Abstract
Alus, the short interspersed repeated sequences (SINEs), are retrotransposons that litter the human genomes and have long been considered junk DNA. However, recent findings that these mobile elements are transcribed, both as distinct RNA polymerase III transcripts and as a part of RNA polymerase II transcripts, suggest biological functions and refute the notion that Alus are biologically unimportant. Indeed, Alu RNAs have been shown to control mRNA processing at several levels, to have complex regulatory functions such as transcriptional repression and modulating alternative splicing and to cause a host of human genetic diseases. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks.
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Affiliation(s)
- Sami Dridi
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA
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Genomic diversity and affinities in population groups of North West India: an analysis of Alu insertion and a single nucleotide polymorphism. Gene 2012; 511:293-9. [PMID: 22995348 DOI: 10.1016/j.gene.2012.08.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/21/2022]
Abstract
The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy-Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity.
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Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, Batzer MA. An Alu-based phylogeny of gibbons (hylobatidae). Mol Biol Evol 2012; 29:3441-50. [PMID: 22683814 DOI: 10.1093/molbev/mss149] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes ∼15-18 Ma. Extant lineages radiated rapidly 6-10 Ma and are organized into four genera (Hylobates, Hoolock, Symphalangus, and Nomascus) consisting of 12-19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock, with the Nomascus-Hoolock clade sister to Hylobates. Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species.
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Affiliation(s)
- Thomas J Meyer
- Department of Biological Sciences, Louisiana State University
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El Moncer W, Bahri R, Esteban E, Abdenni-Guenounou B, Moral P, Ben Chibani J, Chaabani H. Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms. Genet Mol Biol 2011; 34:371-6. [PMID: 21931506 PMCID: PMC3168174 DOI: 10.1590/s1415-47572011005000021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/23/2011] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma) that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample) from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma group at a relatively high frequency. This frequency was similar to that found in sub-Saharans from Nigeria, but significantly different from those found in the Gabes sample and in other North African populations. Our molecular results, consistent with the skin color status, suggest a sub-Saharan origin of this particular Tunisian group.
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Affiliation(s)
- Wifak El Moncer
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 2011; 21:813-20. [PMID: 21632748 PMCID: PMC3106314 DOI: 10.1101/gr.110528.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
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Affiliation(s)
- David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
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DADA RIMA, SARASWATHY KALLURNAVA, MEITEI KHANGEMBAMSOMIBABU, MONDAL PRAKASHRANJAN, KAUR HARPREET, KUCHERIA KIRAN, BHARDWAJ SEEMA, IDRIS GAZNAVI. Genetic sketch of the six population groups of Rajasthan: a study based on 12 autosomal loci. ANTHROPOL SCI 2011. [DOI: 10.1537/ase.100826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RIMA DADA
- Department of Anatomy, All India Institute of Medical Sciences, Delhi
| | | | | | | | | | - KIRAN KUCHERIA
- Department of Anatomy, All India Institute of Medical Sciences, Delhi
| | | | - GAZNAVI IDRIS
- Department of Anatomy, All India Institute of Medical Sciences, Delhi
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Grechko VV, Kosushkin SA, Borodulina OR, Butaeva FG, Darevsky IS. Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 316B:212-26. [PMID: 21462315 DOI: 10.1002/jez.b.21391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 11/08/2022]
Abstract
Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed.
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Affiliation(s)
- Vernata V Grechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Gómez-Pérez L, Alfonso-Sánchez MA, Dipierri JE, Alfaro E, García-Obregón S, De Pancorbo MM, Bailliet G, Peña JA. Microevolutionary processes due to landscape features in the province of Jujuy (Argentina). Am J Hum Biol 2010; 23:177-84. [PMID: 21319246 DOI: 10.1002/ajhb.21098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 08/03/2010] [Accepted: 08/09/2010] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES We seek to evaluate the influence of a diverse and rugged physical environment on the genetic background of human populations. METHODS We analyzed eight polymorphic Alu insertions in 226 individuals from Jujuy province (Argentina), which is composed of several regions with well-defined geographical features and marked contrasts between them associated with differences in altitude (range: 700-3300 m). This regional division was used to assess the spatial variation of the Alu diversity. RESULTS Deviations from Hardy-Weinberg Equilibrium expectations resulting from heterozygous deficit were found for FXIIIB and PV92 in the highest subpopulations. Several Alu elements showed genetic heterogeneity between the highest region (La Puna) and the lowest regions (Valle and Selva). Similarly, a decreasing trend of the average heterozygosity according to altitude was found. Both the centroid method and the admixture analysis unveiled a gene flow above the average in lowland populations, indicating a higher proportion of foreign genes introduced by immigrants of European and African ancestry. Furthermore, several Alu frequency clines fitting the orientation of the altitude gradient were detected. CONCLUSIONS Our study reveals a spatial patterning of the Alu diversity in Jujuy, most likely determined by disparities in landscape and environmental features between the different subregions. Differences in the physical environment would have drastically reduced the homogenizing effects of the gene flow and would have promoted genetic drift episodes in the highest subpopulations. Microevolutionary processes detected in Jujuy have played an important role in the shaping of the gene pool of the populations from this sub-Andean zone from Argentina.
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Affiliation(s)
- Luis Gómez-Pérez
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Bilbao, Spain
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Stepanov VA. Genomes, populations and diseases: ethnic genomics and personalized medicine. Acta Naturae 2010; 2:15-30. [PMID: 22649660 PMCID: PMC3347589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
This review discusses the progress of ethnic genetics, the genetics of common diseases, and the concepts of personalized medicine. We show the relationship between the structure of genetic diversity in human populations and the varying frequencies of Mendelian and multifactor diseases. We also examine the population basis of pharmacogenetics and evaluate the effectiveness of pharmacotherapy, along with a review of new achievements and prospects in personalized genomics.
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Affiliation(s)
- V A Stepanov
- Research Institute for Medical Genetics, Siberian Branch, Russian Academy of Medical Sciences
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48
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Chen Z, Yang G. Novel CHR-2 SINE subfamilies and t-SINEs identified in cetaceans using nonradioactive Southern blotting. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0044-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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McEvoy BP, Lind JM, Wang ET, Moyzis RK, Visscher PM, van Holst Pellekaan SM, Wilton AN. Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry. Am J Hum Genet 2010; 87:297-305. [PMID: 20691402 DOI: 10.1016/j.ajhg.2010.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 06/30/2010] [Accepted: 07/16/2010] [Indexed: 12/19/2022] Open
Abstract
Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.
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Affiliation(s)
- Brian P McEvoy
- Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia.
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50
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Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 2010; 11:410. [PMID: 20591181 PMCID: PMC2996938 DOI: 10.1186/1471-2164-11-410] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/30/2010] [Indexed: 11/10/2022] Open
Abstract
Background Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals. Results Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%. Conclusions Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.
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Affiliation(s)
- David J Witherspoon
- Dept. of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA.
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