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Segatto ALA, Diesel JF, Loreto ELS, da Rocha JBT. De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae). Genet Mol Biol 2018; 41:713-721. [PMID: 30043835 PMCID: PMC6136372 DOI: 10.1590/1678-4685-gmb-2017-0264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/03/2018] [Indexed: 12/17/2022] Open
Abstract
The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.
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Affiliation(s)
- Ana Lúcia Anversa Segatto
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - José Francisco Diesel
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M. Correction: The population genetics of human disease: The case of recessive, lethal mutations. PLoS Genet 2018; 14:e1007499. [PMID: 29965964 PMCID: PMC6028076 DOI: 10.1371/journal.pgen.1007499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M. The population genetics of human disease: The case of recessive, lethal mutations. PLoS Genet 2017; 13:e1006915. [PMID: 28957316 PMCID: PMC5619689 DOI: 10.1371/journal.pgen.1006915] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 07/09/2017] [Indexed: 01/08/2023] Open
Abstract
Do the frequencies of disease mutations in human populations reflect a simple balance between mutation and purifying selection? What other factors shape the prevalence of disease mutations? To begin to answer these questions, we focused on one of the simplest cases: recessive mutations that alone cause lethal diseases or complete sterility. To this end, we generated a hand-curated set of 417 Mendelian mutations in 32 genes reported to cause a recessive, lethal Mendelian disease. We then considered analytic models of mutation-selection balance in infinite and finite populations of constant sizes and simulations of purifying selection in a more realistic demographic setting, and tested how well these models fit allele frequencies estimated from 33,370 individuals of European ancestry. In doing so, we distinguished between CpG transitions, which occur at a substantially elevated rate, and three other mutation types. Intriguingly, the observed frequency for CpG transitions is slightly higher than expectation but close, whereas the frequencies observed for the three other mutation types are an order of magnitude higher than expected, with a bigger deviation from expectation seen for less mutable types. This discrepancy is even larger when subtle fitness effects in heterozygotes or lethal compound heterozygotes are taken into account. In principle, higher than expected frequencies of disease mutations could be due to widespread errors in reporting causal variants, compensation by other mutations, or balancing selection. It is unclear why these factors would have a greater impact on disease mutations that occur at lower rates, however. We argue instead that the unexpectedly high frequency of disease mutations and the relationship to the mutation rate likely reflect an ascertainment bias: of all the mutations that cause recessive lethal diseases, those that by chance have reached higher frequencies are more likely to have been identified and thus to have been included in this study. Beyond the specific application, this study highlights the parameters likely to be important in shaping the frequencies of Mendelian disease alleles. What determines the frequencies of disease mutations in human populations? To begin to answer this question, we focus on one of the simplest cases: mutations that cause completely recessive, lethal Mendelian diseases. We first review theory about what to expect from mutation and selection in a population of finite size and generate predictions based on simulations using a plausible demographic scenario of recent human evolution. For a highly mutable type of mutation, transitions at CpG sites, we find that the predictions are close to the observed frequencies of recessive lethal disease mutations. For less mutable types, however, predictions substantially under-estimate the observed frequency. We discuss possible explanations for the discrepancy and point to a complication that, to our knowledge, is not widely appreciated: that there exists ascertainment bias in disease mutation discovery. Specifically, we suggest that alleles that have been identified to date are likely the ones that by chance have reached higher frequencies and are thus more likely to have been mapped. More generally, our study highlights the factors that influence the frequencies of Mendelian disease alleles.
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Affiliation(s)
- Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
- * E-mail:
| | - Ziyue Gao
- Howard Hughes Medical Institution, Stanford University, Stanford, CA, United States of America
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | | | - Yuval B. Simons
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Imran S. Haque
- Counsyl, 180 Kimball Way, South San Francisco, CA, United States of America
| | - Joseph Pickrell
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- New York Genome Center, New York, NY, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- Department of Systems Biology, Columbia University, New York, NY, United States of America
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