Genetic basis of octanoic acid resistance inDrosophila sechellia: functional analysis of a fine-mapped region

Many phytophagous insect species are ecologic specialists that have adapted to utilize a single host plant. Drosophila sechellia is a specialist that utilizes the ripe fruit of Morinda citrifolia, which is toxic to its sibling species, D. simulans. Here we apply multiplexed shotgun genotyping and QTL analysis to examine the genetic basis of resistance to M. citrifolia fruit toxin in interspecific hybrids. We find that at least four dominant and four recessive loci interact additively to confer resistance to the M. citrifolia fruit toxin. These QTL include a dominant locus of large effect on the third chromosome (QTL-IIIsima) that was not detected in previous analyses. The small-effect loci that we identify overlap with regions that were identified in selection experiments with D. simulans on octanoic acid and in QTL analyses of adult resistance to octanoic acid. Our high-resolution analysis sheds new light upon the complexity of M. citrifolia resistance, and suggests that partial resistance to lower levels of M. citrifolia toxin could be passed through introgression from D. sechellia to D. simulans in nature. The identification of a locus of major effect, QTL-IIIsima, is an important step towards identifying the molecular basis of host plant specialization by D. sechellia.

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The genetic basis of larval resistance to a host plant toxin in Drosophila sechellia

Genetics Research ◽

10.1017/s0016672301005298 ◽

2001 ◽

Vol 78 (3) ◽

pp. 225-233 ◽

Cited By ~ 30

Author(s):

CORBIN D. JONES

Keyword(s):

Host Plant ◽

Genetic Basis ◽

Octanoic Acid ◽

Morinda Citrifolia ◽

Fourth Chromosome ◽

Plant Toxin ◽

Factors Affecting ◽

Resistance Factors ◽

Drosophila Sechellia ◽

Close Relatives

The larvae of Drosophila sechellia are highly resistant to octanoic acid, a toxin found in D. sechellia's host plant, Morinda citrifolia. In contrast, close relatives of D. sechellia, D. simulans and D. melanogaster, are not resistant. In a series of interspecific backcrosses, 11 genetic markers were used to map factors affecting egg-to-adult (‘larval’) resistance in D. sechellia. The third chromosome harbours at least one partially dominant resistance factor. The second chromosome carries at least two mostly dominant resistance factors but no recessive factors. However, neither the X chromosome – which contains 20% of D. sechellia's genome – nor the fourth chromosome appear to affect resistance. These data suggest that larval resistance to Morinda toxin may involve only a handful of genes. These results, when compared with a previous analysis of adult resistance to Morinda toxin in D. sechellia, suggest that larval resistance may involve a subset of the genes underlying adult resistance.

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QTL Mapping of a Brazilian Bioethanol Strain Unravels the Cell Wall Protein-Encoding Gene GAS1 as a Major Contributor to Low Ph Tolerance in S. Cerevisiae

10.21203/rs.3.rs-827768/v1 ◽

2021 ◽

Author(s):

Alessandro L V Coradini ◽

Fellipe da Silveira Bezerra de Mello ◽

Monique Furlan ◽

Carla Maneira ◽

Marcello Falsarella Carazzolle ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Architecture ◽

Genetic Basis ◽

Acid Resistance ◽

Low Ph ◽

Susceptible Strain ◽

Yeast Cells ◽

Synonymous Mutation ◽

Major Contributor ◽

Ph Tolerance

Abstract BACKGROUNDSaccharomyces cerevisiae is largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first and second generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background - including low pH tolerance. RESULTSIn this work, we pioneer the use of QTL mapping to uncover the genetic basis that endow industrial strain Pedra-2 (PE-2) with outstanding acid resistance. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome XIII as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed allele GAS1, encoding a β-1,3-glucanosyltransferase, as the major contributor to this phenotype. The GAS1 sequence alignment of 48 S. cerevisiae strains pointed out a non-synonymous mutation (T211A) prevalence in wild type isolates, which is absent in laboratory strains. We further showcase that GAS1 allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process.CONCLUSIONThis work revealed GAS1 as the major causative gene associated with low pH resistance in PE-2, harboring a non-synonymous mutation persistent in industrial strains. We also showcase how GAS1PE-2 can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains for the industrial production of economically-relevant goods. Our results collectively show the importance of tailored industrial isolated strains in the discovery of the genetic architecture of relevant traits and its implications over productivity.

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A potential role for the gut microbiota in the specialisation of Drosophila sechellia to its toxic host noni (Morinda citrifolia)

10.1101/526517 ◽

2019 ◽

Author(s):

Chloe Heys ◽

Adam M Fisher ◽

Andrea D Dewhurst ◽

Zenobia Lewis ◽

Anne Lize

Keyword(s):

Gut Microbiota ◽

Host Plant ◽

Lactobacillus Plantarum ◽

Potential Role ◽

Octanoic Acid ◽

Acid Resistance ◽

Morinda Citrifolia ◽

Risk Of Death ◽

Drosophila Sechellia ◽

Series Of Experiments

Adaptation to a novel food source can have significant evolutionary advantages. The fruit fly, Drosophila sechellia, is a specialist of the toxic plant noni (Morinda citrifolia). Little is known as to how D. sechellia has become resistant to the toxins in the fruit - comprised predominantly of octanoic acid - but to date, the behavioural preferences for the fruit and genetic architecture underlying them, have been well studied. Here, we examine whether the gut microbiota could have played a role in adaptation to the fruit. In the first series of experiments, we examine the gut microbiota of wild-type, laboratory reared flies and characterise the gut microbiota when reared on the natural host plant, versus a standard Drosophila diet. We show a rapid transition in the core bacterial diversity and abundance within this species and discover sole precedence of Lactobacillus plantarum when reared on M. citrifolia. We also discover that flies reared on a laboratory diet are more likely to carry bacterial pathogens such as Bacillus cereus, although their function in Drosophila is unknown. Flies reared on a laboratory diet have a significantly reduced weight but with no impact on the risk of death before adulthood, when compared to the wild noni diet. In the second series of experiments, we examine the potential role of the gut microbiota in adaptation to octanoic acid resistance in this species and its sister species, Drosophila melanogaster, to which the fruit is usually fatal. We use a combination of methods to analyse resistance to octanoic acid by conducting life history analysis, behavioural assays and bacterial analysis in both D. sechellia and D. melanogaster. We find that by creating experimental evolution lines of D. melanogaster supplemented with gut microbiota from D. sechellia, we can decrease D. melanogaster aversion to octanoic acid, with the flies even preferring to feed on food supplemented with the acid. We suggest this represents the first step in the evolutionary and ecological specialisation of D. sechellia to its toxic host plant, and that the gut microbiota, Lactobacillus plantarum in particular, may have played a key role in host specialisation.

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Derived esterase activity in Drosophila sechellia contributes to evolved octanoic acid resistance

Insect Molecular Biology ◽

10.1111/imb.12587 ◽

2019 ◽

Vol 28 (6) ◽

pp. 798-806 ◽

Cited By ~ 2

Author(s):

S. M. Lanno ◽

J. D. Coolon

Keyword(s):

Esterase Activity ◽

Octanoic Acid ◽

Acid Resistance ◽

Drosophila Sechellia

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QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae

Biotechnology for Biofuels ◽

10.1186/s13068-021-02079-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Alessandro L. V. Coradini ◽

Fellipe da Silveira Bezerra de Mello ◽

Monique Furlan ◽

Carla Maneira ◽

Marcelo F. Carazzolle ◽

...

Keyword(s):

Qtl Mapping ◽

Genetic Architecture ◽

Genetic Basis ◽

Productivity Loss ◽

Acid Resistance ◽

Low Ph ◽

Susceptible Strain ◽

Yeast Cells ◽

Ph Tolerance ◽

Food And Beverage

Abstract Background Saccharomyces cerevisiae is largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first- and second-generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background—including low pH tolerance. Results In this work, we pioneer the use of QTL mapping to uncover the genetic basis that confers to the industrial strain Pedra-2 (PE-2) acidic tolerance during growth at low pH. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome X as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed the allele GAS1, encoding a β-1,3-glucanosyltransferase, as the casual variant in this region. The GAS1 sequence alignment of distinct S. cerevisiae strains pointed out a non-synonymous mutation (A631G) prevalence in wild-type isolates, which is absent in laboratory strains. We further showcase that GAS1 allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process. Conclusion This work revealed GAS1 as one of the main causative genes associated with tolerance to growth at low pH in PE-2. We also showcase how GAS1PE-2 can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains. Our results collectively show the importance of tailored industrial isolated strains in discovering the genetic architecture of relevant traits and its implications over productivity.

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Versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems

10.1101/2021.03.19.436125 ◽

2021 ◽

Author(s):

Jing Li ◽

Eric Galvez ◽

Lena Amend ◽

Eva Almasi ◽

Aida Iljazovic ◽

...

Keyword(s):

Functional Analysis ◽

Genetic Basis ◽

Vegan Diet ◽

Type Ii ◽

Human Gut ◽

Health States ◽

Genetic Studies ◽

Genetic Tools ◽

Allelic Exchange ◽

Polysaccharide Utilization Loci

Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant-rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs), and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan-processing PULs (PULAra) and that the type-II PULAra is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in the future.

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Evolutionary and Functional Analysis of Coagulase Positivity among the Staphylococci

mSphere ◽

10.1128/msphere.00381-21 ◽

2021 ◽

Author(s):

Amy C. Pickering ◽

Gonzalo Yebra ◽

Xiangyu Gong ◽

Mariya I. Goncheva ◽

Bryan A. Wee ◽

...

Keyword(s):

Functional Analysis ◽

Genetic Basis ◽

Comprehensive Analysis ◽

Evolutionary Genetic

The ability of some species of staphylococci to promote coagulation of plasma is a key pathogenic and diagnostic trait. Here, we provide a comprehensive analysis of the coagulase positivity of the staphylococci and its evolutionary genetic basis.

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Genome sequencing and functional analysis of an environmental isolate Escherichia coli Cont-1 revealed its genetic basis of arsenic-transformation and niche adaptation

Ecological Genetics and Genomics ◽

10.1016/j.egg.2018.11.001 ◽

2018 ◽

Vol 9 ◽

pp. 34-42 ◽

Cited By ~ 1

Author(s):

Balaram Mohapatra ◽

Pinaki Sar

Keyword(s):

Escherichia Coli ◽

Functional Analysis ◽

Genome Sequencing ◽

Genetic Basis ◽

Environmental Isolate ◽

Niche Adaptation ◽

Arsenic Transformation

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Genomics analysis of hexanoic acid exposure in Drosophila species

10.1101/2021.06.08.447576 ◽

2021 ◽

Author(s):

Joseph D. Coolon ◽

Zachary Drum ◽

Stephen Lanno ◽

Sara Gregory ◽

Serena Shimshak ◽

...

Keyword(s):

Octanoic Acid ◽

Acid Resistance ◽

Hexanoic Acid ◽

Morinda Citrifolia ◽

Ecological Communities ◽

Transcriptional Responses ◽

Dietary Specialization ◽

Generalist Species ◽

Seychelles Islands ◽

High Concentrations

Drosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium chain fatty acid volatiles that deter and are toxic to generalist insects D. sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in <D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions.

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