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Kumar A, Pal A, Singh P, Rani I, Tondolo V, Rongioletti M, Squitti R. Might Diet, APOE-APOA1 Axis, and Iron Metabolism Provide Clues About the Discrepancy in Alzheimer's Disease Occurrence Between Humans and Chimpanzees? A Bioinformatics-Based Re-Analysis of Gene Expression Data on Mice Fed with Human and Chimpanzee Diets. Biol Trace Elem Res 2024; 202:3750-3759. [PMID: 37938458 DOI: 10.1007/s12011-023-03932-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
The emergence of conflicting reports on the natural occurrence of Alzheimer's disease (AD) in non-human primates has prompted research on the comparison of the role of diet-associated changes in gene expression between humans and non-human primates. This article analyzes the effects of different human and chimpanzee diets and their link with apolipoproteins, lipid, and iron (Fe) metabolism, starting from available data, to find out any gap in the existing knowledge. By using a system biology approach, we have re-analyzed the liver and brain RNA seq data of mice fed with either human or chimpanzee diet for 2 weeks to look for genetic differences that may explain the differences in AD occurrence between those two classes. In liver samples of mice fed with the chimpanzee diet in comparison to the human diet, apolipoprotein A-1, ceruloplasmin, and 10 other genes were upregulated while 21 genes were downregulated. However, brain apolipoprotein E4 gene expression was not changed upon diet. Genetic, structural, and functional differences in apolipoprotein E protein, along with differences in Fe metabolisms and a longer lifespan of humans during evolution may account for the observed disparity.
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Affiliation(s)
- Ashok Kumar
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Amit Pal
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Kalyani, West Bengal, 741245, India.
| | - Parminder Singh
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Isha Rani
- Department of Biochemistry, Maharishi Markandeshwar College of Medical Sciences and Research (MMCMSR), Sadopur, Ambala, India
| | - Vincenzo Tondolo
- Digestive and Colorectal Surgery, Ospedale Isola Tiberina, Gemelli Isola, 00186, Rome, Italy
- Digestive Surgery Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Mauro Rongioletti
- Department of Laboratory Science, Ospedale Isola Tiberina, Gemelli Isola, 00186, Rome, Italy
| | - Rosanna Squitti
- Department of Laboratory Science, Ospedale Isola Tiberina, Gemelli Isola, 00186, Rome, Italy
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Chao KH, Heinz JM, Hoh C, Mao A, Shumate A, Pertea M, Salzberg SL. Combining DNA and protein alignments to improve genome annotation with LiftOn. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.593026. [PMID: 38798552 PMCID: PMC11118573 DOI: 10.1101/2024.05.16.593026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely-related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species. LiftOn's protein-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies where they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honey bee, rice, and Arabidopsis thaliana. It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and D. erecta.
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Affiliation(s)
- Kuan-Hao Chao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jakob M. Heinz
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Celine Hoh
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alan Mao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alaina Shumate
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mihaela Pertea
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
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3
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Heins DC, Moody KN, Arostegui MC, Harmon BS, Blum MJ, Quinn TP. Distinct evolutionary lineages of Schistocephalus parasites infecting co-occurring sculpin and stickleback fishes in Alaska. Parasitology 2024; 151:626-633. [PMID: 38719483 DOI: 10.1017/s0031182024000593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [s.d.] = 15) and stickleback (mean = 86; s.d. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.
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Affiliation(s)
- David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Kristine N Moody
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Martin C Arostegui
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98103, USA
| | - Brian S Harmon
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98103, USA
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98103, USA
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Belay S, Belay G, Nigussie H, Jian-Lin H, Tijjani A, Ahbara AM, Tarekegn GM, Woldekiros HS, Mor S, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci Data 2024; 11:139. [PMID: 38287052 PMCID: PMC10825132 DOI: 10.1038/s41597-024-02973-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species' evolutionary trajectory.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Tigray, Ethiopia.
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia.
| | - Helen Nigussie
- Addis Ababa University, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- ILRI-CAAS Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
| | - Abdulfatai Tijjani
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Siobhan Mor
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- School of Philosophical and Historical Inquiry, University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Olivier Hanotte
- LiveGene Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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5
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Kosuthova K, Solc R. Inversions on human chromosomes. Am J Med Genet A 2023; 191:672-683. [PMID: 36495134 DOI: 10.1002/ajmg.a.63063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Human chromosome inversions are types of balanced structural variations, making them difficult to analyze. Thanks to PEM (paired-end sequencing and mapping), there has been tremendous progress in studying inversions. Inversions play an important role as an evolutionary factor, contributing to the formation of gonosomes, speciation of chimpanzees and humans, and inv17q21.3 or inv8p23.1 exhibit the features of natural selection. Both inversions have been related to pathogenic phenotype by directly affecting a gene structure (e.g., inv5p15.1q14.1), regulating gene expression (e.g., inv7q21.3q35) and by predisposing to other secondary arrangements (e.g., inv7q11.23). A polymorphism of human inversions is documented by the InvFEST database (a database that stores information about clinical predictions, validations, frequency of inversions, etc.), but only a small fraction of these inversions is validated, and a detailed analysis is complicated by the frequent location of breakpoints within regions of repetitive sequences.
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Affiliation(s)
- Klara Kosuthova
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
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6
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Bergman J, Schierup MH. Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes. Genome Biol 2022; 23:215. [PMID: 36253794 PMCID: PMC9575207 DOI: 10.1186/s13059-022-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences. RESULTS We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis. CONCLUSIONS Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.
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Affiliation(s)
- Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
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7
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Crawford MA, Wang Y, Marsh DE, Johnson MR, Ogundipe E, Ibrahim A, Rajkumar H, Kowsalya S, Kothapalli KSD, Brenna JT. Neurodevelopment, nutrition and genetics. A contemporary retrospective on neurocognitive health on the occasion of the 100th anniversary of the National Institute of Nutrition, Hyderabad, India. Prostaglandins Leukot Essent Fatty Acids 2022; 180:102427. [PMID: 35413515 PMCID: PMC9152880 DOI: 10.1016/j.plefa.2022.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/03/2022] [Indexed: 11/28/2022]
Abstract
In celebration of the centenary of the National Institute of Nutrition (NIN), Hyderabad, India (1918-2018), a symposium highlighted the progress in nutrition knowledge made over the century, as well as major gaps in implementation of that knowledge. Brain famine caused by a shortage of nutrients required for perinatal brain development has unfortunately become a global reality, even as protein-calorie famine was largely averted by the development of high yield crops. While malnutrition remains widespread, the neglect of global food policies that support brain development and maintenance are most alarming. Brain disorders now top the list of the global burden of disease, even with obesity rising throughout the world. Neurocognitive health, remarkably, is seldom listed among the non-communicable diseases (NCDs) and is therefore seldom considered as a component of food policy. Most notably, the health of mothers before conception and through pregnancy as mediated by proper nutrition has been neglected by the current focus on early death in non-neurocognitive NCDs, thereby compromising intellectual development of the ensuing generations. Foods with balanced essential fatty acids and ample absorbable micronutrients are plentiful for populations with access to shore-based foods, but deficient only a few kilometres away from the sea. Sustained access to brain supportive foods is a priority for India and throughout the world to enable each child to develop to their intellectual potential, and support a prosperous, just, and peaceful world. Nutrition education and food policy should place the nutritional requirements for the brain on top of the list of priorities.
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Affiliation(s)
- Michael A Crawford
- Institute of Brain Chemistry and Human Nutrition, Chelsea and Westminster Hospital Campus of Imperial College, London, United Kingdom
| | - Yiqun Wang
- Institute of Brain Chemistry and Human Nutrition, Chelsea and Westminster Hospital Campus of Imperial College, London, United Kingdom
| | - David E Marsh
- Institute of Brain Chemistry and Human Nutrition, Chelsea and Westminster Hospital Campus of Imperial College, London, United Kingdom
| | - Mark R Johnson
- Institute of Brain Chemistry and Human Nutrition, Chelsea and Westminster Hospital Campus of Imperial College, London, United Kingdom
| | - Enitan Ogundipe
- Institute of Brain Chemistry and Human Nutrition, Chelsea and Westminster Hospital Campus of Imperial College, London, United Kingdom
| | - Ahamed Ibrahim
- National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - Hemalatha Rajkumar
- National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India
| | - S Kowsalya
- Department of Food Science and Nutrition, Avinashilingam Institute for Home Science and Higher Education for Women (Deemed to be University), Coimbatore, India
| | - Kumar S D Kothapalli
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723, United States.
| | - J T Brenna
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723, United States.
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8
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Medhat B, Shawish A. FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for DNA-Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1924-1936. [PMID: 31976902 DOI: 10.1109/tcbb.2020.2967385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper introduces a novel alignment-free sequence analysis methodology. Its main idea is based on introducing a new representation of the DNA-Sequence. This representation breaks the dependency between the DNA bases that exist in the traditional string presentation. We called it the Four-Lists-Representation (FLR). Based on the FLR, a series of revolutionary algorithms for searching, map-discovery, similarity-score analysis, and similarity-visualization have been developed. They are combined in what we call the FLR Methodology. The paper also studies most of the available similarity analysis techniques in a comprehensive state-of-art review. The conducted extensive simulation and theoretical studies confirm the outperformance of the whole set of FLR-based algorithms in terms of speed and memory consumption in comparison to a long list of available similarity analysis algorithms. The ability to provide a similarity-map, similarity-score, and similarity-graph as a set of evidence-based rationales makes the quality of results provided by the proposed methodology presents a new edge in this field and promises a new area of genome-based research.
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9
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Sarkar BK, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Chakraborty C. Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter. Sci Rep 2021; 11:13701. [PMID: 34211040 PMCID: PMC8249421 DOI: 10.1038/s41598-021-93154-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.
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Affiliation(s)
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, College of Medicine, Chuncheon-si, Gangwon-do, 24252, Republic of Korea
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha, 756020, India
| | - Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, College of Medicine, Chuncheon-si, Gangwon-do, 24252, Republic of Korea.
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore, Rd, Jagannathpur, Kolkata, West Bengal, 700126, India.
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Silliman K, Indorf JL, Knowlton N, Browne WE, Hurt C. Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama. BMC Ecol Evol 2021; 21:104. [PMID: 34049492 PMCID: PMC8164322 DOI: 10.1186/s12862-021-01836-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01836-3.
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Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA. .,Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Jane L Indorf
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Carla Hurt
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Department of Biology, Tennessee Tech University, Cookeville, TN, 38505, USA
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11
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Large-scale analysis of 2,152 Ig-seq datasets reveals key features of B cell biology and the antibody repertoire. Cell Rep 2021; 35:109110. [PMID: 33979623 DOI: 10.1016/j.celrep.2021.109110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibody repertoire sequencing enables researchers to acquire millions of B cell receptors and investigate these molecules at the single-nucleotide level. This power and resolution in studying humoral responses have led to its wide applications. However, most of these studies were conducted with a limited number of samples. Given the extraordinary diversity, assessment of these key features with a large sample set is demanded. Thus, we collect and systematically analyze 2,152 high-quality heavy-chain antibody repertoires. Our study reveals that 52 core variable genes universally contribute to more than 99% of each individual's repertoire; a distal interspersed preferences characterize V gene recombination; the number of public clones between two repertoires follows a linear model, and the positive selection dominates at RGYW motif in somatic hypermutations. Thus, this population-level analysis resolves some critical features of the antibody repertoire and may have significant value to the large cadre of scientists.
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12
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DiseaseLinc: Disease Enrichment Analysis of Sets of Differentially Expressed LincRNAs. Cells 2021; 10:cells10040751. [PMID: 33805436 PMCID: PMC8065951 DOI: 10.3390/cells10040751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/17/2022] Open
Abstract
Long intergenic non-coding RNAs (LincRNAs) are long RNAs that do not encode proteins. Functional evidence is lacking for most of them. Their biogenesis is not well-known, but it is thought that many lincRNAs originate from genomic duplication of coding material, resulting in pseudogenes, gene copies that lose their original function and can accumulate mutations. While most pseudogenes eventually stop producing a transcript and become erased by mutations, many of these pseudogene-based lincRNAs keep similarity to the parental gene from which they originated, possibly for functional reasons. For example, they can act as decoys for miRNAs targeting the parental gene. Enrichment analysis of function is a powerful tool to discover the functional effects of a treatment producing differential expression of transcripts. However, in the case of lincRNAs, since their function is not easy to define experimentally, such a tool is lacking. To address this problem, we have developed an enrichment analysis tool that focuses on lincRNAs exploiting their functional association, using as a proxy function that of the parental genes and has a focus on human diseases.
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13
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Zhou J, Zhang M, Li X, Wang Z, Pan D, Shi Y. Performance comparison of four types of target enrichment baits for exome DNA sequencing. Hereditas 2021; 158:10. [PMID: 33597004 PMCID: PMC7888174 DOI: 10.1186/s41065-021-00171-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-generation sequencing technology is developing rapidly and target capture sequencing has become an important technique. Several different platforms for library preparation and target capture with different bait types respectively are commercially available. Here we compare the performance of the four platforms with different bait types to find out their advantages and limitations. The purpose of this study is to help investigators and clinicians select the appropriate platform for their particular application and lay the foundation for the development of a better target capture platform for next-generation sequencing. RESULTS We formulate capture efficiency as a novel parameter that can be used to better evaluations of specificity and coverage depth among the different capture platforms. Target coverage, capture efficiency, GC bias, AT Dropout, sensitivity in single nucleotide polymorphisms, small insertions and deletions detection, and the feature of each platform were compared for low input samples. In general, all platforms perform well and small differences among them are revealed. In our results, RNA baits have stronger binding power than DNA baits, and with ultra deep sequencing, double stranded RNA baits perform better than single stranded RNA baits in all aspects. DNA baits got better performance in the region with high GC content and RNA baits got lower AT dropout suggesting that the binding power is different between DNA and RNA baits to genome regions with different characteristics. CONCLUSIONS The platforms with double stranded RNA baits have the most balanced capture performance. Our results show the key differences in performance among the four updated platforms with four different bait types. The better performance of double stranded RNA bait with ultra deep sequencing suggests that it may improve the sensitivity of ultra low frequent mutation detection. In addition, we further propose that the mixed baits of double stranded RNA and single stranded DNA may improve target capture performance.
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Grants
- 2017YFC0908105, 2019YFA0905400 the National Key R&D Program of China
- 2017SHZDZX01 Shanghai Municipal Science and Technology Major Project
- U1804284, 81421061, 81701321, 32070679, 81501154 the Natural Science Foundation of China
- 15XD1502200 the Program of Shanghai Subject Chief Scientist
- 13dz2260500 the National Program for Support of Top-Notch Young Professionals, Shanghai Key Laboratory of Psychotic Disorders
- SHDC12016115 the National Program for Support of Top-Notch Young Professionals, Shanghai Hospital Development Center
- 17JC1402900, 17490712200, 18DZ2260200 Shanghai Municipal Commission of Science and Technology
- ZK2015B01, 201540114 shanghai municipal health commission
- 19X150010012 Scientific Research and Development Fund of Shanghai Jiao Tong University
- the National Key R&D Program of China
- the National Program for Support of Top-Notch Young Professionals, Shanghai Hospital Development Center
- shanghai municipal health commission
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Affiliation(s)
- Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Mancang Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Xiaoqi Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
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14
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Suntsova MV, Buzdin AA. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics 2020; 21:535. [PMID: 32912141 PMCID: PMC7488140 DOI: 10.1186/s12864-020-06962-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5-7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species.
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Affiliation(s)
- Maria V Suntsova
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia
| | - Anton A Buzdin
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia. .,Omicsway Corp, Walnut, CA, USA. .,Moscow Institute of Physics and Technology (National Research University), 141700, Moscow, Russia.
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15
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Jumaa RS, Allawi AB, Jabbar RN. Genetic Analysis of Field Isolates of Infectious Bursal Disease Virus in Iraqi Farms. THE IRAQI JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.30539/ijvm.v44i1.931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Sixty samples of bursa of Fabricius were collected from broiler chickens suspected to be infected with infectious bursal disease virus (IBDV) in different areas of Iraq for molecular evaluation. The extracted nucleic acid was amplified using reverse transcriptase polymerase chain reaction (RT-PCR) targeting genes of segment A (Vp2, Vp3, Vp4 and Vp5 genes) and segment B (VP1 genes). The products of amplification were sent to Korea for sequencing using Sanger method. The sequencing analysis of the IBDV from the Iraqi isolates revealed that each gene had different transition and transversion (nonsense and missense of point mutation) compared to reference genes. The phylogenetic tree analysis showed that the VP2 of segment A of the Iraqi samples was similar to that of an Egyptian strain with 96%similarity, the polypeptide VP2-3-4 of segment A of the Iraqi samples was similar to those of a Chinese strain with 99% similarity and the VP5 of segment A was similar to that of Chinese strain with 99% similarity. However, the phylogenetic tree analysis showed that the VP1 of segment B had 95% similarity with that of a Chinese strain.
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16
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Baradaran-Rafii A, Sarvari M, Alavi-Moghadam S, Payab M, Goodarzi P, Aghayan HR, Larijani B, Rezaei-Tavirani M, Biglar M, Arjmand B. Cell-based approaches towards treating age-related macular degeneration. Cell Tissue Bank 2020; 21:339-347. [PMID: 32157501 DOI: 10.1007/s10561-020-09826-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022]
Abstract
Age-related macular degeneration as one of the most common causes of worldwide vision loss needs a proper approach for treatment. Therein, cell therapy and regenerative medicine can hold a great promise to be an effective approach. Accordingly, some preclinical and clinical studies were conducted to search around the therapeutic influence of stem cells in Age-related macular degeneration models and subjects. Hereupon, the purpose of the current review is to discuss the mechanisms of age-related macular degeneration, appropriate animal models along with suitable dosage and route of stem cell administration for its treatment.
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Affiliation(s)
- Alireza Baradaran-Rafii
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Sarvari
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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17
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Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma. Genetics 2020; 214:809-823. [PMID: 32079595 DOI: 10.1534/genetics.120.303028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Methylated cytosines deaminate at higher rates than unmethylated cytosines, and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.
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18
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Lee K, Park TIH, Heppner P, Schweder P, Mee EW, Dragunow M, Montgomery JM. Human in vitro systems for examining synaptic function and plasticity in the brain. J Neurophysiol 2020; 123:945-965. [PMID: 31995449 DOI: 10.1152/jn.00411.2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The human brain shows remarkable complexity in its cellular makeup and function, which are distinct from nonhuman species, signifying the need for human-based research platforms for the study of human cellular neurophysiology and neuropathology. However, the use of adult human brain tissue for research purposes is hampered by technical, methodological, and accessibility challenges. One of the major problems is the limited number of in vitro systems that, in contrast, are readily available from rodent brain tissue. With recent advances in the optimization of protocols for adult human brain preparations, there is a significant opportunity for neuroscientists to validate their findings in human-based systems. This review addresses the methodological aspects, advantages, and disadvantages of human neuron in vitro systems, focusing on the unique properties of human neurons and synapses in neocortical microcircuits. These in vitro models provide the incomparable advantage of being a direct representation of the neurons that have formed part of the human brain until the point of recording, which cannot be replicated by animal models nor human stem-cell systems. Important distinct cellular mechanisms are observed in human neurons that may underlie the higher order cognitive abilities of the human brain. The use of human brain tissue in neuroscience research also raises important ethical, diversity, and control tissue limitations that need to be considered. Undoubtedly however, these human neuron systems provide critical information to increase the potential of translation of treatments from the laboratory to the clinic in a way animal models are failing to provide.
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Affiliation(s)
- Kevin Lee
- Department of Physiology, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, University of Auckland, New Zealand
| | - Thomas I-H Park
- Centre for Brain Research, University of Auckland, New Zealand.,Department of Pharmacology, University of Auckland, Auckland, New Zealand
| | - Peter Heppner
- Centre for Brain Research, University of Auckland, New Zealand.,Department of Neurosurgery, Auckland City Hospital, Auckland, New Zealand
| | - Patrick Schweder
- Centre for Brain Research, University of Auckland, New Zealand.,Department of Neurosurgery, Auckland City Hospital, Auckland, New Zealand
| | - Edward W Mee
- Centre for Brain Research, University of Auckland, New Zealand.,Department of Neurosurgery, Auckland City Hospital, Auckland, New Zealand
| | - Michael Dragunow
- Centre for Brain Research, University of Auckland, New Zealand.,Department of Pharmacology, University of Auckland, Auckland, New Zealand
| | - Johanna M Montgomery
- Department of Physiology, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, University of Auckland, New Zealand
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19
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Zhou JL, Xu J, Jiao AG, Yang L, Chen J, Callac P, Liu Y, Wang SX. Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom. Front Microbiol 2019; 10:2686. [PMID: 31803173 PMCID: PMC6877668 DOI: 10.3389/fmicb.2019.02686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022] Open
Abstract
The polymerase chain reaction (PCR) is widely used in modern biology and medicine. However, PCR artifacts can complicate the interpretation of PCR-based results. The internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster is the consensus fungal barcode marker and suspected PCR artifacts have been reported in many studies, especially for the analyses of environmental fungal samples. At present, the patterns of PCR artifacts in the whole fungal ITS region (ITS1+5.8S+ITS2) are not known. In this study, we analyzed the error rates of PCR at three template complexity levels using the divergent copies of ITS from the mushroom Agaricus subrufescens. Our results showed that PCR using the Phusion® High-Fidelity DNA Polymerase has a per nucleotide error rate of about 4 × 10–6 per replication. Among the detected mutations, transitions were much more frequent than transversions, insertions, and deletions. When divergent alleles were mixed as templates in the same reaction, a significant proportion (∼30%) of recombinant molecules were detected. The in vitro mixed-template results were comparable to those obtained from using the genomic DNA of the original mushroom specimen as template. Our results indicate that caution should be in place when interpreting ITS sequences from individual fungal specimens, especially those containing divergent ITS copies. Similar results could also happen to PCR-based analyses of other multicopy DNA fragments as well as single-copy DNA sequences with divergent alleles in diploid organisms.
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Affiliation(s)
- Jun-Liang Zhou
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China.,International Exchange and Cooperation Department, Kunming University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - An-Guo Jiao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Li Yang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Jie Chen
- Instituto de Ecología, Veracruz, Mexico
| | | | - Yu Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
| | - Shou-Xian Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing, China
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20
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Talyan S, Andrade-Navarro MA, Muro EM. Identification of transcribed protein coding sequence remnants within lincRNAs. Nucleic Acids Res 2019; 46:8720-8729. [PMID: 29986053 PMCID: PMC6158594 DOI: 10.1093/nar/gky608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences. Importantly, such elements are known to be tissue-specifically expressed and to play a widespread role in gene regulation across thousands of genomic loci. However, very little is known of the mechanisms for the evolutionary biogenesis of these RNA elements, especially given their poor conservation across species. It has been proposed that lincRNAs might arise from pseudogenes. To test this systematically, we developed a novel method that searches for remnants of protein-coding sequences within lincRNA transcripts; the hypothesis is that we can trace back their biogenesis from protein-coding genes or posterior transposon/retrotransposon insertions. Applying this method, we found 203 human lincRNA genes with regions significantly similar to protein-coding sequences. Our method provides a visualization tool to trace the evolutionary biogenesis of lincRNAs with respect to protein-coding genes by sequence divergence. Subsequently, we show the expression correlation between lincRNAs and their identified parental protein-coding genes using public RNA-seq repositories, hinting at novel gene regulatory relationships. In summary, we developed a novel computational methodology to study non-coding gene sequences, which can be applied to identify the evolutionary biogenesis and function of lincRNAs.
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Affiliation(s)
- Sweta Talyan
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Enrique M Muro
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
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21
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Farnoud F, Schwartz M, Bruck J. Estimation of duplication history under a stochastic model for tandem repeats. BMC Bioinformatics 2019; 20:64. [PMID: 30727948 PMCID: PMC6364452 DOI: 10.1186/s12859-019-2603-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/03/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of the same pattern in tandem repeats and their high variability, they contain a wealth of information about the mutations that have led to their formation. The ability to extract this information can enhance our understanding of evolutionary mechanisms. RESULTS We present a stochastic model for the formation of tandem repeats via tandem duplication and substitution mutations. Based on the analysis of this model, we develop a method for estimating the relative mutation rates of duplications and substitutions, as well as the total number of mutations, in the history of a tandem repeat sequence. We validate our estimation method via Monte Carlo simulation and show that it outperforms the state-of-the-art algorithm for discovering the duplication history. We also apply our method to tandem repeat sequences in the human genome, where it demonstrates the different behaviors of micro- and mini-satellites and can be used to compare mutation rates across chromosomes. It is observed that chromosomes that exhibit the highest mutation activity in tandem repeat regions are the same as those thought to have the highest overall mutation rates. However, unlike previous works that rely on comparing human and chimpanzee genomes to measure mutation rates, the proposed method allows us to find chromosomes with the highest mutation activity based on a single genome, in essence by comparing (approximate) copies of the pattern in tandem repeats. CONCLUSION The prevalence of tandem repeats in most organisms and the efficiency of the proposed method enable studying various aspects of the formation of tandem repeats and the surrounding sequences in a wide range of settings. AVAILABILITY The implementation of the estimation method is available at http://ips.lab.virginia.edu/smtr .
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Affiliation(s)
- Farzad Farnoud
- Department of Electrical and Computer Engineering, Department of Computer Science, University of Virginia, Charlottesville, USA
| | - Moshe Schwartz
- Department of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jehoshua Bruck
- Department of Electrical Engineering, California Institute of Technology, Pasadena, USA
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22
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Appropriate Assignment of Fossil Calibration Information Minimizes the Difference between Phylogenetic and Pedigree Mutation Rates in Humans. Life (Basel) 2018; 8:life8040049. [PMID: 30360410 PMCID: PMC6316143 DOI: 10.3390/life8040049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/18/2018] [Accepted: 10/18/2018] [Indexed: 12/24/2022] Open
Abstract
Studies that measured mutation rates in human populations using pedigrees have reported values that differ significantly from rates estimated from the phylogenetic comparison of humans and chimpanzees. Consequently, exchanges between mutation rate values across different timescales lead to conflicting divergence time estimates. It has been argued that this variation of mutation rate estimates across hominoid evolution is in part caused by incorrect assignment of calibration information to the mean coalescent time among loci, instead of the true genetic isolation (speciation) time between humans and chimpanzees. In this study, we investigated the feasibility of estimating the human pedigree mutation rate using phylogenetic data from the genomes of great apes. We found that, when calibration information was correctly assigned to the human⁻chimpanzee speciation time (and not to the coalescent time), estimates of phylogenetic mutation rates were statistically equivalent to the estimates previously reported using studies of human pedigrees. We conclude that, within the range of biologically realistic ancestral generation times, part of the difference between whole-genome phylogenetic and pedigree mutation rates is due to inappropriate assignment of fossil calibration information to the mean coalescent time instead of the speciation time. Although our results focus on the human⁻chimpanzee divergence, our findings are general, and relevant to the inference of the timescale of the tree of life.
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23
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Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, Nordborg M. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat Genet 2017; 49:1705-1713. [PMID: 29083404 PMCID: PMC5709169 DOI: 10.1038/ng.3980] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/27/2017] [Indexed: 12/16/2022]
Abstract
Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.
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Affiliation(s)
- Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Department of Neurology, University of California Los Angeles, USA
| | - Yu Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | | | | | - Vasily Ramensky
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Martin Antonio
- Medical Research Council (MRC), The Gambia Unit, The Gambia
| | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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24
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Krasovec M, Eyre-Walker A, Sanchez-Ferandin S, Piganeau G. Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes. Mol Biol Evol 2017; 34:1770-1779. [PMID: 28379581 PMCID: PMC5455958 DOI: 10.1093/molbev/msx119] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mutation is the ultimate source of genetic variation, and knowledge of mutation rates is fundamental for our understanding of all evolutionary processes. High throughput sequencing of mutation accumulation lines has provided genome wide spontaneous mutation rates in a dozen model species, but estimates from nonmodel organisms from much of the diversity of life are very limited. Here, we report mutation rates in four haploid marine bacterial-sized photosynthetic eukaryotic algae; Bathycoccus prasinos, Ostreococcus tauri, Ostreococcus mediterraneus, and Micromonas pusilla. The spontaneous mutation rate between species varies from μ = 4.4 × 10-10 to 9.8 × 10-10 mutations per nucleotide per generation. Within genomes, there is a two-fold increase of the mutation rate in intergenic regions, consistent with an optimization of mismatch and transcription-coupled DNA repair in coding sequences. Additionally, we show that deviation from the equilibrium GC content increases the mutation rate by ∼2% to ∼12% because of a GC bias in coding sequences. More generally, the difference between the observed and equilibrium GC content of genomes explains some of the inter-specific variation in mutation rates.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Adam Eyre-Walker
- Evolution, behaviour and environment, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sophie Sanchez-Ferandin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls/Mer, France
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25
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Targeted sequencing of both DNA strands barcoded and captured individually by RNA probes to identify genome-wide ultra-rare mutations. Sci Rep 2017; 7:3356. [PMID: 28611392 PMCID: PMC5469810 DOI: 10.1038/s41598-017-03448-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/05/2017] [Indexed: 12/13/2022] Open
Abstract
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq). This method combines an ultra-sensitive single-stranded library construction with barcoding error correction, termed DEEPER-Library; and a DNA capture approach using RNA probes targeting both DNA strands, termed DEEPER-Capture. DEEPER-Seq can create NGS libraries from as little as 20 pg DNA with PCR error correcting capabilities, and capture target sequences at an average ratio of 29.2% by targeting both DNA strands simultaneously with an over 98.6% coverage. Our method tags and sequences each of the two strands of a DNA duplex independently and only scores mutations that are found at the same position in both strands, which allows us to identify mutations with allelic fractions down to 0.03% in a whole exome sequencing (WES) study with a background error rate of one artificial error per 4.8 × 109 nucleotides.
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26
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Powers MS, Smith PH, McKee SA, Ehringer MA. From sexless to sexy: Why it is time for human genetics to consider and report analyses of sex. Biol Sex Differ 2017; 8:15. [PMID: 28473910 PMCID: PMC5415751 DOI: 10.1186/s13293-017-0136-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
Science has come a long way with regard to the consideration of sex differences in clinical and preclinical research, but one field remains behind the curve: human statistical genetics. The goal of this commentary is to raise awareness and discussion about how to best consider and evaluate possible sex effects in the context of large-scale human genetic studies. Over the course of this commentary, we reinforce the importance of interpreting genetic results in the context of biological sex, establish evidence that sex differences are not being considered in human statistical genetics, and discuss how best to conduct and report such analyses. Our recommendation is to run stratified analyses by sex no matter the sample size or the result and report the findings. Summary statistics from stratified analyses are helpful for meta-analyses, and patterns of sex-dependent associations may be hidden in a combined dataset. In the age of declining sequencing costs, large consortia efforts, and a number of useful control samples, it is now time for the field of human genetics to appropriately include sex in the design, analysis, and reporting of results.
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Affiliation(s)
- Matthew S. Powers
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309 USA
| | - Phillip H. Smith
- Department of Community Health and Social Medicine, CUNY School of Medicine, New York, NY 10031 USA
| | - Sherry A. McKee
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06519 USA
| | - Marissa A. Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309 USA
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27
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Nemzer LR. A binary representation of the genetic code. Biosystems 2017; 155:10-19. [PMID: 28300609 DOI: 10.1016/j.biosystems.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
Abstract
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed. Using a principal component analysis, it is shown that the physicochemical properties of amino acids related to protein folding also correlate with certain bit positions of their respective labels. Thus, the likelihood for a point mutation to be conservative, and less likely to cause a change in protein functionality, can be estimated.
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Affiliation(s)
- Louis R Nemzer
- Department of Chemistry and Physics, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
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28
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Boussaha M, Michot P, Letaief R, Hozé C, Fritz S, Grohs C, Esquerré D, Duchesne A, Philippe R, Blanquet V, Phocas F, Floriot S, Rocha D, Klopp C, Capitan A, Boichard D. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genet Sel Evol 2016; 48:87. [PMID: 27846802 PMCID: PMC5111192 DOI: 10.1186/s12711-016-0268-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. Results In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. Conclusions To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Pauline Michot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Amandine Duchesne
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Philippe
- GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France
| | | | - Florence Phocas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandrine Floriot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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29
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Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium. J Genet 2016; 94:731-40. [PMID: 26690529 DOI: 10.1007/s12041-015-0588-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide a means for assessing concerns regarding SNP array-based GWAS findings as well as for realistically bounding expectations for next generation sequencing (NGS)-based GWAS. We calculated and compared base composition, transitions to transversions ratio, minor allele frequency and heterozygous rate for SNPs from HapMap and 1KGP for the 622 common individuals. We analysed the genotype discordance between HapMap and 1KGP to assess consistency in the SNPs from the two references. In 1KGP, 90.58% of 36,817,799 SNPs detected were not measured in HapMap. More SNPs with minor allele frequencies less than 0.01 were found in 1KGP than HapMap. The two references have low disc ordance (generally smaller than 0.02) in genotypes of common SNPs, with most discordance from heterozygous SNPs. Our study demonstrated that SNP array-based GWAS findings were reliable and useful, although only a small portion of genetic variances were explained. NGS can detect not only common but also rare variants, supporting the expectation that NGS-based GWAS will be able to incorporate a much larger portion of genetic variance than SNP arrays-based GWAS.
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30
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Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome. PLoS One 2016; 11:e0163990. [PMID: 27736909 PMCID: PMC5063475 DOI: 10.1371/journal.pone.0163990] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.
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31
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Wu H, Liu YH, Wang GD, Yang CT, Otecko NO, Liu F, Wu SF, Wang L, Yu L, Zhang YP. Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome. Sci Rep 2016; 6:35004. [PMID: 27713520 PMCID: PMC5054530 DOI: 10.1038/srep35004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 09/22/2016] [Indexed: 12/31/2022] Open
Abstract
Genome-wide studies on high-altitude adaptation have received increased attention as a classical case of organismal evolution under extreme environment. However, the current genetic understanding of high-altitude adaptation emanated mainly from autosomal analyses. Only a few earlier genomic studies paid attention to the allosome. In this study, we performed an intensive scan of the X chromosome of public genomic data generated from Tibetan Mastiff (TM) and five other dog populations for indications of high-altitude adaptation. We identified five genes showing signatures of selection on the X chromosome. Notable among these genes was angiomotin (AMOT), which is related to the process of angiogenesis. We sampled additional 11 dog populations (175 individuals in total) at continuous altitudes in China from 300 to 4,000 meters to validate and test the association between the haplotype frequency of AMOT gene and altitude adaptation. The results suggest that AMOT gene may be a notable candidate gene for the adaptation of TM to high-altitude hypoxic conditions. Our study shows that X chromosome deserves consideration in future studies of adaptive evolution.
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Affiliation(s)
- Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, China
| | - Yan-Hu Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chun-Tao Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Fei Liu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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32
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Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, Rai K, Uranw S, Bhattarai NR, Khanal B, Prajapati VK, Sharma S, Stark O, Schönian G, De Koning HP, Settimo L, Vanhollebeke B, Roy S, Ostyn B, Boelaert M, Maes L, Berriman M, Dujardin JC, Cotton JA. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife 2016; 5. [PMID: 27003289 PMCID: PMC4811772 DOI: 10.7554/elife.12613] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/15/2016] [Indexed: 12/25/2022] Open
Abstract
Leishmania donovani causes visceral leishmaniasis (VL), the second most deadly vector-borne parasitic disease. A recent epidemic in the Indian subcontinent (ISC) caused up to 80% of global VL and over 30,000 deaths per year. Resistance against antimonial drugs has probably been a contributing factor in the persistence of this epidemic. Here we use whole genome sequences from 204 clinical isolates to track the evolution and epidemiology of L. donovani from the ISC. We identify independent radiations that have emerged since a bottleneck coincident with 1960s DDT spraying campaigns. A genetically distinct population frequently resistant to antimonials has a two base-pair insertion in the aquaglyceroporin gene LdAQP1 that prevents the transport of trivalent antimonials. We find evidence of genetic exchange between ISC populations, and show that the mutation in LdAQP1 has spread by recombination. Our results reveal the complexity of L. donovani evolution in the ISC in response to drug treatment. DOI:http://dx.doi.org/10.7554/eLife.12613.001 The parasite Leishmania donovani causes a disease called visceral leishmaniasis that affects many of the world's poorest people. Around half a million new cases develop every year, but health authorities lack safe and effective drugs to treat them. Up to 80% of these cases occur in the Indian subcontinent, where devastating epidemics have occurred in the last decades. One reason these epidemics continue to occur is that the parasites develop genetic mutations allowing them to adapt to and resist the drugs used to kill them. As there are few existing drugs that can kill L. donovani, it is crucial to understand how drug resistance emerges and spreads among parasite populations. Imamura, Downing, Van den Broeck et al. have now investigated the history of visceral leishmaniasis epidemics by characterising the complete genetic sequence – or genome – of 204 L. donovani parasite samples. This revealed that the majority of parasites in the Indian subcontinent first appeared in the nineteenth century, matching the first historical records of visceral leishmaniasis epidemics. The genomes show that most of the parasites are genetically similar and can be clustered into several closely related groups. These groups first appeared in the 1960s following the end of a regional campaign to eradicate malaria. The most common parasite group is particularly resistant to drugs called antimonials, which were the main treatment for leishmaniasis until recently. These parasites have a small genetic change that scrambles most of a protein known to be involved in the uptake of antimonials. Parasites may also be able to develop resistance to drugs through additional mechanisms that allow them to produce many copies of the same gene. These mechanisms could allow the parasites to rapidly adapt to new drugs or changes in the populations it infects. The work of Imamura et al. looks only at parasites isolated from patients then grown in the laboratory, so further research is now needed to explore how variable the Leishmania genome is in both of the parasite’s hosts: humans and sandflies. Imamura et al.’s study reveals how L. donovani has spread throughout the Indian subcontinent in fine detail. The genome data can be used to create simple molecular tools that could form an "early warning system" to track the success of disease control programs and to determine how well the current drugs are working. DOI:http://dx.doi.org/10.7554/eLife.12613.002
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Affiliation(s)
- Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tim Downing
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Galway, Ireland
| | | | | | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - An Mannaert
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Manu Vanaerschot
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maya Berg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Géraldine De Muylder
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Franck Dumetz
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Saskia Decuypere
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Keshav Rai
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | | | | | - Vijay Kumar Prajapati
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Smriti Sharma
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Olivia Stark
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Schönian
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Harry P De Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luca Settimo
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Benoit Vanhollebeke
- Laboratory of Molecular Parasitology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Syamal Roy
- Department of Infectious Diseases and Immunology, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India
| | - Bart Ostyn
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marleen Boelaert
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Louis Maes
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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33
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Mendes FK, Hahn MW. Gene Tree Discordance Causes Apparent Substitution Rate Variation. Syst Biol 2016; 65:711-21. [DOI: 10.1093/sysbio/syw018] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/23/2016] [Indexed: 01/01/2023] Open
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34
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García-García G, Baux D, Faugère V, Moclyn M, Koenig M, Claustres M, Roux AF. Assessment of the latest NGS enrichment capture methods in clinical context. Sci Rep 2016; 6:20948. [PMID: 26864517 PMCID: PMC4750071 DOI: 10.1038/srep20948] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022] Open
Abstract
Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.
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Affiliation(s)
- Gema García-García
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Valérie Faugère
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mélody Moclyn
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Michel Koenig
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
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35
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Huang X, Yan HD, Zhang XQ, Zhang J, Frazier TP, Huang DJ, Lu L, Huang LK, Liu W, Peng Y, Ma X, Yan YH. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species. FRONTIERS IN PLANT SCIENCE 2016; 7:496. [PMID: 27148320 PMCID: PMC4834353 DOI: 10.3389/fpls.2016.00496] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 03/29/2016] [Indexed: 05/11/2023]
Abstract
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.
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Affiliation(s)
- Xiu Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Hai-Dong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Xin-Quan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Jian Zhang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal SciencesChongqing, China
- Jian Zhang
| | - Taylor P. Frazier
- Department of Horticulture, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - De-Jun Huang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal SciencesChongqing, China
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de BarcelonaCerdanyola del Vallès, Spain
| | - Lin-Kai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Lin-Kai Huang
| | - Wei Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
| | - Yan-Hong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversityChengdu, China
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Win NZ, Choi EY, Jang DJ, Park J, Park JK. Molecular comparison of the genus Junonia (Lepidoptera: Nymphalidae) in Myanmar. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2015. [DOI: 10.1016/j.japb.2015.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Joshi S, Tolkunov D, Aviv H, Hakimi AA, Yao M, Hsieh JJ, Ganesan S, Chan CS, White E. The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis. Cell Rep 2015; 13:1895-908. [PMID: 26655904 PMCID: PMC4779191 DOI: 10.1016/j.celrep.2015.10.059] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/28/2015] [Accepted: 10/19/2015] [Indexed: 12/26/2022] Open
Abstract
Oncocytomas are predominantly benign neoplasms possessing pathogenic mitochondrial mutations and accumulation of respiration-defective mitochondria, characteristics of unknown significance. Using exome and transcriptome sequencing, we identified two main subtypes of renal oncocytoma. Type 1 is diploid with CCND1 rearrangements, whereas type 2 is aneuploid with recurrent loss of chromosome 1, X or Y, and/or 14 and 21, which may proceed to more aggressive eosinophilic chromophobe renal cell carcinoma (ChRCC). Oncocytomas activate 5' adenosine monophosphate-activated protein kinase (AMPK) and Tp53 (p53) and display disruption of Golgi and autophagy/lysosome trafficking, events attributed to defective mitochondrial function. This suggests that the genetic defects in mitochondria activate a metabolic checkpoint, producing autophagy impairment and mitochondrial accumulation that limit tumor progression, revealing a novel tumor-suppressive mechanism for mitochondrial inhibition with metformin. Alleviation of this metabolic checkpoint in type 2 by p53 mutations may allow progression to eosinophilic ChRCC, indicating that they represent higher risk.
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Affiliation(s)
- Shilpy Joshi
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Denis Tolkunov
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Hana Aviv
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, One Robert Wood Johnson Place, MEB 212, New Brunswick, NJ 08901, USA
| | - Abraham A Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Ming Yao
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 1 Robert Wood Johnson Place, New Brunswick, NJ 08901, USA
| | - Chang S Chan
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 1 Robert Wood Johnson Place, New Brunswick, NJ 08901, USA.
| | - Eileen White
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA.
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Daniel C, Behm M, Öhman M. The role of Alu elements in the cis-regulation of RNA processing. Cell Mol Life Sci 2015; 72:4063-76. [PMID: 26223268 PMCID: PMC11113721 DOI: 10.1007/s00018-015-1990-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 01/18/2023]
Abstract
The human genome is under constant invasion by retrotransposable elements. The most successful of these are the Alu elements; with a copy number of over a million, they occupy about 10 % of the entire genome. Interestingly, the vast majority of these Alu insertions are located in gene-rich regions, and one-third of all human genes contains an Alu insertion. Alu sequences are often embedded in gene sequence encoding pre-mRNAs and mature mRNAs, usually as part of their intron or UTRs. Once transcribed, they can regulate gene expression as well as increase the number of RNA isoforms expressed in a tissue or a species. They also regulate the function of other RNAs, like microRNAs, circular RNAs, and potentially long non-coding RNAs. Mechanistically, Alu elements exert their effects by influencing diverse processes, such as RNA editing, exonization, and RNA processing. In so doing, they have undoubtedly had a profound effect on human evolution.
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Affiliation(s)
- Chammiran Daniel
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden
| | - Mikaela Behm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 106 91, Stockholm, Sweden.
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Pranckevičiene E, Rančelis T, Pranculis A, Kučinskas V. Challenges in exome analysis by LifeScope and its alternative computational pipelines. BMC Res Notes 2015; 8:421. [PMID: 26346699 PMCID: PMC4562342 DOI: 10.1186/s13104-015-1385-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 08/24/2015] [Indexed: 12/22/2022] Open
Abstract
Background Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze sequencing data. NGS tools for Illumina platforms are well documented which is not the case with AB SOLiD systems. We applied several computational and variant calling pipelines to analyse targeted exome sequencing data obtained using AB SOLiD 5500 system. Our investigated tools comprised proprietary LifeScope’s pipeline in combination with open source color-space competent mapping programs and a variant caller. We present instrumental details of the pipelines that were used and quantitative comparative analysis of variant lists generated by LifeScope’s pipeline versus open source tools. Results Sufficient coverage of targeted regions was achieved by all investigated pipelines. High variability was observed in identities of variants across the mapping programs. We observed less than 50 % concordance of variant lists produced by approaches based on different mapping algorithms. We summarized different approaches with regards to coverage (DP) and quality (QUAL) properties of the variants provided by GATK and found that LifeScope’s computational pipeline is superior. Fusion of information on mapping profiles (pileup) at genomic positions of variants in several different alignments proved to be a useful strategy to assess questionable singleton variants. Conclusions We quantitatively supported a conclusion that Lifescope’s pipeline is superior for processing sequencing data obtained by AB SOLiD 5500 system. Nevertheless the use of alternative pipelines is encouraged because aggregation of information from other mapping and variant calling approaches helps to resolve questionable calls and increases the confidence of the call. It was noted that a coverage threshold for variant to be considered for further analysis has to be chosen in data-driven way to prevent a loss of important information.
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Affiliation(s)
- Erinija Pranckevičiene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu str. 2, LT-08661, Vilnius, Lithuania.
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu str. 2, LT-08661, Vilnius, Lithuania.
| | - Aidas Pranculis
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu str. 2, LT-08661, Vilnius, Lithuania.
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu str. 2, LT-08661, Vilnius, Lithuania.
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Kuroda K, Kiyono T, Eitsuka T, Isogai H, Takahashi K, Donai K, Isogai E, Fukuda T. Establishment of cell lines derived from the genus Macaca through controlled expression of cell cycle regulators. J Cell Biochem 2015; 116:205-11. [PMID: 25187009 DOI: 10.1002/jcb.24963] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/29/2014] [Indexed: 11/06/2022]
Abstract
Nonhuman primates are useful animal models for the study of human diseases. However, the number of established cell lines from nonhuman primates is quite limited compared with the number established from other experimental animals. The establishment of nonhuman primate cell lines would allow drug testing on those cell lines before moving experiments into primates. In this study, we established nonhuman primate primary cell lines by introducing the genes for CDK4R24C, cyclin D1, and hTERT. These cell lines proliferated more rapidly than primary cells and bypassed cellular senescence. Karyotype analysis showed that the chromosome patterns were intact in the immortalized cell lines. Furthermore, we showed that the expression of introduced genes could be precisely controlled through the Tet-Off system with the addition of doxycycline. The present study shows that introduction of the CDK4R24C, cyclin D1, and hTERT genes are effective methods of establishing nonhuman primate cell lines.
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Affiliation(s)
- Kengo Kuroda
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-amamiyamachi, Aoba-ku, Sendai, 981-8555, Japan
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Maudhoo MD, Madison JD, Norgren RB. De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences. Gigascience 2015; 4:18. [PMID: 25897398 PMCID: PMC4403674 DOI: 10.1186/s13742-015-0061-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the species most closely related to humans. For this reason, it is especially important to have complete and accurate chimpanzee nucleotide and protein sequences to understand how humans evolved their unique capabilities. We provide transcriptome data from four untransformed cell types derived from the reference Pan troglodytes, "Clint", to better annotate the chimpanzee genome and provide empirical validation for proposed gene models of this important species. FINDINGS RNA was extracted from primary cells cultured from four tissues: skin, adipose stroma, vascular smooth muscle and skeletal muscle. These four RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly (TSA) database. CONCLUSIONS We have provided a high quality annotation of 44,275 transcripts with full-length coding sequence (CDS). This set represented a total of 10,110 unique genes, thus providing empirical support for their existence. This dataset can be used to improve the annotation of the Pan troglodytes genome.
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Affiliation(s)
- Mnirnal D Maudhoo
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 USA
| | - Jacob D Madison
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 USA
| | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 USA
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Ng J, Trask JS, Houghton P, Smith DG, Kanthaswamy S. Use of genome-wide heterospecific single-nucleotide polymorphisms to estimate linkage disequilibrium in rhesus and cynomolgus macaques. Comp Med 2015; 65:62-9. [PMID: 25730759 PMCID: PMC4396931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 10/27/2014] [Indexed: 06/04/2023]
Abstract
Rhesus and cynomolgus macaques are frequently used in biomedical research, and the availability of their reference genomes now provides for their use in genome-wide association studies. However, little is known about linkage disequilibrium (LD) in their genomes, which can affect the design and success of such studies. Here we studied LD by using 1781 conserved single-nucleotide polymorphisms (SNPs) in 183 rhesus macaques (Macaca mulatta), including 97 purebred Chinese and 86 purebred Indian animals, and 96 cynomolgus macaques (M. fascicularis fascicularis). Correlation between loci pairs decayed to 0.02 at 1146.83, 2197.92, and 3955.83 kb for Chinese rhesus, Indian rhesus, and cynomolgus macaques, respectively. Differences between the observed heterozygosity and minor allele frequency (MAF) of pairs of these 3 taxa were highly statistically significant. These 3 nonhuman primate taxa have significantly different genetic diversities (heterozygosity and MAF) and rates of LD decay. Our study confirms a much lower rate of LD decay in Indian than in Chinese rhesus macaques relative to that previously reported. In contrast, the especially low rate of LD decay in cynomolgus macaques suggests the particular usefulness of this species in genome-wide association studies. Although conserved markers, such as those used here, are required for valid LD comparisons among taxa, LD can be assessed with less bias by using species-specific markers, because conserved SNPs may be ancestral and therefore not informative for LD.
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Affiliation(s)
- Jillian Ng
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, California, USA
| | - Jessica Satkoski Trask
- Molecular Anthropology Laboratory, California National Primate Research Center, University of California, Davis, California, USA
| | | | - David G Smith
- Molecular Anthropology Laboratory, Department of Anthropology, California National Primate Research Center, University of California, Davis, California, USA
| | - Sree Kanthaswamy
- Molecular Anthropology Laboratory, Department of Anthropology, California National Primate Research Center, Department of Environmental Toxicology, University of California, Davis, USA; California, School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, Arizona, USA.
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Partha R, Raman K. Revisiting robustness and evolvability: evolution in weighted genotype spaces. PLoS One 2014; 9:e112792. [PMID: 25390641 PMCID: PMC4229248 DOI: 10.1371/journal.pone.0112792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Robustness and evolvability are highly intertwined properties of biological systems. The relationship between these properties determines how biological systems are able to withstand mutations and show variation in response to them. Computational studies have explored the relationship between these two properties using neutral networks of RNA sequences (genotype) and their secondary structures (phenotype) as a model system. However, these studies have assumed every mutation to a sequence to be equally likely; the differences in the likelihood of the occurrence of various mutations, and the consequence of probabilistic nature of the mutations in such a system have previously been ignored. Associating probabilities to mutations essentially results in the weighting of genotype space. We here perform a comparative analysis of weighted and unweighted neutral networks of RNA sequences, and subsequently explore the relationship between robustness and evolvability. We show that assuming an equal likelihood for all mutations (as in an unweighted network), underestimates robustness and overestimates evolvability of a system. In spite of discarding this assumption, we observe that a negative correlation between sequence (genotype) robustness and sequence evolvability persists, and also that structure (phenotype) robustness promotes structure evolvability, as observed in earlier studies using unweighted networks. We also study the effects of base composition bias on robustness and evolvability. Particularly, we explore the association between robustness and evolvability in a sequence space that is AU-rich – sequences with an AU content of 80% or higher, compared to a normal (unbiased) sequence space. We find that evolvability of both sequences and structures in an AU-rich space is lesser compared to the normal space, and robustness higher. We also observe that AU-rich populations evolving on neutral networks of phenotypes, can access less phenotypic variation compared to normal populations evolving on neutral networks.
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Affiliation(s)
- Raghavendran Partha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- * E-mail:
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Baes CF, Dolezal MA, Koltes JE, Bapst B, Fritz-Waters E, Jansen S, Flury C, Signer-Hasler H, Stricker C, Fernando R, Fries R, Moll J, Garrick DJ, Reecy JM, Gredler B. Evaluation of variant identification methods for whole genome sequencing data in dairy cattle. BMC Genomics 2014; 15:948. [PMID: 25361890 PMCID: PMC4289218 DOI: 10.1186/1471-2164-15-948] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/14/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and high-density single nucleotide variant (SNV) arrays. RESULTS The total number of SNVs identified varied by software and method, with single (multi) sample results ranging from 17.7 to 22.0 (16.9 to 22.0) million variants. Computing time varied considerably between software. Preparatory realignment of insertions and deletions and subsequent base quality score recalibration had only minor effects on the number and quality of SNVs identified by different software, but increased computing time considerably. Average concordance for single (multi) sample results with high-density chip data was 58.3% (87.0%) and average genotype concordance in correctly identified SNVs was 99.2% (99.2%) across software. The average quality of SNVs identified, measured as the ratio of transitions to transversions, was higher using single sample methods than multi sample methods. A consensus approach using results of different software generally provided the highest variant quality in terms of transition/transversion ratio. CONCLUSIONS Our findings serve as a reference for variant identification pipeline development in non-human organisms and help assess the implication of preparatory steps in next-generation sequencing pipelines for organisms with incomplete reference genomes (pipeline code is included). Benchmarking this information should prove particularly useful in processing next-generation sequencing data for use in genome-wide association studies and genomic selection.
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Affiliation(s)
- Christine F Baes
- Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, CH-3052 Zollikofen, Switzerland.
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Ségurel L, Wyman MJ, Przeworski M. Determinants of Mutation Rate Variation in the Human Germline. Annu Rev Genomics Hum Genet 2014; 15:47-70. [DOI: 10.1146/annurev-genom-031714-125740] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laure Ségurel
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206, Muséum National d'Histoire Naturelle–Centre National de la Recherche Scientifique–Université Paris 7 Diderot, Paris 75231, France;
| | - Minyoung J. Wyman
- Department of Biological Sciences, Columbia University, New York, NY 10027;
| | - Molly Przeworski
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637;
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Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids. J Mol Evol 2014; 78:307-9. [PMID: 24916657 DOI: 10.1007/s00239-014-9627-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
Abstract
We propose that glycine was the first amino acid to be incorporated into the genetic code, followed by serine, aspartic and/or glutamic acid-small hydrophilic amino acids that all have codons in the bottom right-hand corner of the standard genetic code table. Because primordial ribosomal synthesis is presumed to have been rudimentary, this stage would have been characterized by the synthesis of short, water-soluble peptides, the first of which would have comprised polyglycine. Evolution of the code is proposed to have occurred by the duplication and mutation of tRNA sequences, which produced a radiation of codon assignment outwards from the bottom right-hand corner. As a result of this expansion, we propose a trend from small hydrophilic to hydrophobic amino acids, with selection for longer polypeptides requiring a hydrophobic core for folding and stability driving the incorporation of hydrophobic amino acids into the code.
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Chilamakuri CSR, Lorenz S, Madoui MA, Vodák D, Sun J, Hovig E, Myklebost O, Meza-Zepeda LA. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 2014; 15:449. [PMID: 24912484 PMCID: PMC4092227 DOI: 10.1186/1471-2164-15-449] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen's SeqCap EZ v3.0, Agilent's SureSelect v4.0, Illumina's TruSeq Exome, and Illumina's Nextera Exome, all applied to the same human tumor DNA sample. RESULTS Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content. CONCLUSIONS We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.
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Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. BMC Bioinformatics 2014; 15:125. [PMID: 24884706 PMCID: PMC4098776 DOI: 10.1186/1471-2105-15-125] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/16/2014] [Indexed: 12/12/2022] Open
Abstract
Background Genotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not explicitly filtered by the standard GATK Variant Quality Score Recalibration (VQSR) tool and thus remain a source of errors in whole exome sequencing (WES) projects that follow GATK’s recommended best practices. Therefore, additional data filtering methods are required to effectively remove these errors before performing association analyses with complex phenotypes. Here we empirically derive thresholds for genotype and variant filters that, when used in conjunction with the VQSR tool, achieve higher data quality than when using VQSR alone. Results The detailed filtering strategies improve the concordance of sequenced genotypes with array genotypes from 99.33% to 99.77%; improve the percent of discordant genotypes removed from 10.5% to 69.5%; and improve the Ti/Tv ratio from 2.63 to 2.75. We also demonstrate that managing batch effects by separating samples based on different target capture and sequencing chemistry protocols results in a final data set containing 40.9% more high-quality variants. In addition, imputation is an important component of WES studies and is used to estimate common variant genotypes to generate additional markers for association analyses. As such, we demonstrate filtering methods for imputed data that improve genotype concordance from 79.3% to 99.8% while removing 99.5% of discordant genotypes. Conclusions The described filtering methods are advantageous for large population-based WES studies designed to identify common and rare variation associated with complex diseases. Compared to data processed through standard practices, these strategies result in substantially higher quality data for common and rare association analyses.
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Cantarel BL, Weaver D, McNeill N, Zhang J, Mackey AJ, Reese J. BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity. BMC Bioinformatics 2014; 15:104. [PMID: 24725768 PMCID: PMC3999887 DOI: 10.1186/1471-2105-15-104] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/31/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Accurate genomic variant detection is an essential step in gleaning medically useful information from genome data. However, low concordance among variant-calling methods reduces confidence in the clinical validity of whole genome and exome sequence data, and confounds downstream analysis for applications in genome medicine.Here we describe BAYSIC (BAYeSian Integrated Caller), which combines SNP variant calls produced by different methods (e.g. GATK, FreeBayes, Atlas, SamTools, etc.) into a more accurate set of variant calls. BAYSIC differs from majority voting, consensus or other ad hoc intersection-based schemes for combining sets of genome variant calls. Unlike other classification methods, the underlying BAYSIC model does not require training using a "gold standard" of true positives. Rather, with each new dataset, BAYSIC performs an unsupervised, fully Bayesian latent class analysis to estimate false positive and false negative error rates for each input method. The user specifies a posterior probability threshold according to the user's tolerance for false positive and false negative errors; lowering the posterior probability threshold allows the user to trade specificity for sensitivity while raising the threshold increases specificity in exchange for sensitivity. RESULTS We assessed the performance of BAYSIC in comparison to other variant detection methods using ten low coverage (~5X) samples from The 1000 Genomes Project, a tumor/normal exome pair (40X), and exome sequences (40X) from positive control samples previously identified to contain clinically relevant SNPs. We demonstrated BAYSIC's superior variant-calling accuracy, both for somatic mutation detection and germline variant detection. CONCLUSIONS BAYSIC provides a method for combining sets of SNP variant calls produced by different variant calling programs. The integrated set of SNP variant calls produced by BAYSIC improves the sensitivity and specificity of the variant calls used as input. In addition to combining sets of germline variants, BAYSIC can also be used to combine sets of somatic mutations detected in the context of tumor/normal sequencing experiments.
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Muntané G, Horvath JE, Hof PR, Ely JJ, Hopkins WD, Raghanti MA, Lewandowski AH, Wray GA, Sherwood CC. Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission. ACTA ACUST UNITED AC 2014; 25:1596-607. [PMID: 24408959 DOI: 10.1093/cercor/bht354] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Increased relative brain size characterizes the evolution of primates, suggesting that enhanced cognition plays an important part in the behavioral adaptations of this mammalian order. In addition to changes in brain anatomy, cognition can also be regulated by molecular changes that alter synaptic function, but little is known about modifications of synapses in primate brain evolution. The aim of the current study was to investigate the expression patterns and evolution of 20 synaptic genes from the prefrontal cortex of 12 primate species. The genes investigated included glutamate receptors, scaffolding proteins, synaptic vesicle components, as well as factors involved in synaptic vesicle release and structural components of the nervous system. Our analyses revealed that there have been significant changes during primate brain evolution in the components of the glutamatergic signaling pathway in terms of gene expression, protein expression, and promoter sequence changes. These results could entail functional modifications in the regulation of specific genes related to processes underlying learning and memory.
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Affiliation(s)
- Gerard Muntané
- Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | - Julie E Horvath
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27707, USA North Carolina Museum of Natural Sciences, Nature Research Center, Raleigh, NC 27601, USA Department of Biology, NC Central University, Durham, NC 27707, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 New York Consortium for Primate Evolution, New York, NY 10024, USA
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, NM 88330, USA
| | - William D Hopkins
- Neuroscience Institute and Language Research Center, Georgia State University, Atlanta, GA 30302, USA
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA
| | | | - Gregory A Wray
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27707, USA Biology Department, Duke University, Durham, NC, USA
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC 20052, USA
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