DNA sequencing of Cochineal bug to save the families of rural producers

By Vinicius Maracaja-Coutinho, PhD / Beagle Bioinformatics, Universidad Mayor

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Cochineal bugs are decimating a cactus that is the main source of food for cattle during long periods of drought in the Brazilian Northeast region. It’s drastically affecting the environment, population  and local economy. The genome analysis of the bug is of key importance in order to find new ways to control the plague and that’s what we intend to do with your help.

The main problem:

The insects of the specie Dactylopius opuntiae (Hemiptera, Dactylopiidae), commonly known as Cochineal bug, decimated, in the last 10 years, the crops of Drooping Prickly Pear cactus (Opuntia monacantha) in the Northeast region of Brazil. This cactus is the main source of food for cattle in the region, the poorest and driest in the country, due to its resistance in long droughts periods. Besides, since last year the region is experiencing its worst drought in the last forty years, which has directly affected the lives of residents and local farmers. Along with this long period of drought and the decimation of the cactus, the cattle have been suffering losses, which provoked a damage of 250 million dollars to small farmers only in the state of Paraíba. All of this is affecting the population in the region, since the cattle is being eradicated, and consequently reducing the production of milk and meat, resulting in a serious problem of hunger.

The cochineal bug is widely used on the production of red dyes for cosmetics, food and pharmaceutical industries. However, about 10 years ago some local farmers brought the wrong species to Brazilian Northeast. Instead of Dactylopius coccus, they brought Dactylopius opuntiae, which produces a low-quality dye and is highly detrimental to the cactus, acting as a plague.

sertao

The Northeast is one of the poorest regions in Brazil, with a population of approximately 55 million inhabitants and the lowest social-economic rates in the country. Lands in desertification process cover most of its geographic territory and the economy of the region is mostly based on cattle and goats. According to the IBGE (Brazilian Institute of Geography and Statistics), the state of Paraíba, one of the 9 states in the region, had the biggest reduction of cattle in the country in 2012, a loss of 407.201 animals, resulting in the official declaration of Emergency State in around 170 cities by the State Government of Paraíba. This scenery didn’t change in the last 3 years.

cochonilha

This situation made many institutions mobilize themselves to find solutions to the problem. One example is the revitalization project of the cactus from the National Institute of Semi-Arid, INSA, which is currently testing three species of the cactus resistant to Cochineal. However, despite the importance of these initiatives, the solutions are palliative and do not work in a definitive way.

Brazilian TV presenting the drought and Cochineal problem on the state of Paraíba.

What’s the solution we are proposing?

Our project involves to analyze the genome of the Cochineal bug as a way to find means to control the animal. The genome is the whole genetic material of a living organism. Elucidating the complete genome sequence of an organism can make possible the identification of its complete repertoire of genes.

problemxsolutionGenes are genetic subunits that contain the information necessary to generate the functional elements that are involved in all the cellular mechanisms of a complex organism: proteins and RNAs. Having this catalog of genes in our hands, we are able to elucidate all the metabolic pathways involved in each molecular process of the bug, including the potential targets for an effective control of the animal.

The main goal of our project is to elucidate the repertoire of all genes and biochemical pathways of the insect. The idea is provide a catalogue of potential targets that will help to stop in a definitive way the decimation of the plant and to help improving the situation in the Northeast of Brazil. The creation of this catalogue is the first step to be able to control efficiently the insect and solve the problem in the region.

How are we going to do this?

  1. The first step is to collect the Cochineal bug and extract its DNA. This step will be done in partnership with the Instituto Vandique (www.institutovandique.org.br) and the Universidade Federal da Paraíba (www.ufpb.br) in João Pessoa.
  1. The second step is to create an in vitro “library” with all the sequences/fragments of the insect DNA. This library is important because it will be representing all the genetic material to be sequenced.
  1. The third step will be the sequencing of the samples. Here, we will start to decode the cochineal genetic material. We will use the Illumina HiSeq sequencing approach, outsourced in third-part companies. The result of this process will be a sea of sequence data that will be further analyzed by bioinformatics approaches.
  1. The fourth and last step is the analysis of the data generated after sequencing. This step will be done in collaboration by the Bioinformatics team from Beagle Bioinformatics, Instituto Vandique and Universidad Mayor. Here, we will identify and characterize the complete repertoire of genes and metabolic pathways in the Cochineal bug, that will lead to the elucidation of the potential targets for the animal control. Note that all data generated will be be made freely available and accessible for the whole community.

In another words, what we will do is find potential targets to control the insect by sequencing and analyzing its genes. That’s a much more efficient way to solve the problem than the others solutions tried until this day.

How will the funds be used:

The funds will be used in the first tree steps of the Project. It will be US$ 200.00 for the DNA extraction and genomic Library construction and US$ 2,800.00  DNA sequencing using  Illumina HiSeq approach. Adding Dodo and PayPal fees, the total costs is US$ 3,300.00 Dollars.

costs

If you contribute with this campaign you will receive rewards:

  1. Donating US$5 you will receive a personal Thank You in your Facebook timeline;
  2. Donating US$10 your name will apear on the Acknowledgements in our final open database www.cochinealgenome.com;
  3. Donating US$25 you will receive the above-mentioned reward, plus a digital sticker “I am part of the Cochineal Genome Project”;
  4. Donating US$50 you will receive the above-mentioned rewards, plus a digital illustration of all genes identified on the Cochineal genome. (Note that this illustration will be made available after the genome analysis);
  5. Donating US$100 you will receive the above-mentioned rewards, plus a Skype meeting with our team;
  6. Donating US$200 you will receive the above-mentioned rewards, plus your name (or your company’s name) on the Acknowledgements of all publications generated by this research;
  7. Donating US$500 you will receive the above-mentioned rewards, plus a visit to the Laboratory of Integrative Bioinformatics, in Santiago (Chile). Travel costs not included;
  8. Donating US$1,000 you will receive all above-mentioned Rewards, plus a guided visit to the Cariri Region in Paraíba, Brasil (housing provided for free in a local farm, travel costs not included).

Remember why it is important: 

The Cochineal bug has been destroying completely, for the last 10 years, the main food for cattle and goats in periods of drought in northeastern Brazil. Having the repertoire of genes of this insect sequenced will be important to elucidate all the molecular mechanisms behind the animal biology. It can lead us to identify all the molecular targets for the control of this plague. It will not give an end to the drought in the region, but will ease the situation for local population, avoiding the death of a number of animals, that have the cactus in their diet and, consequently, the hunger of local communities. Additionally, it can be of big importance for the local economy, based on the agriculture and livestock.

Open Data, Open Access, Open Science!

We remember you that all data obtained on this project will be published in an open access journal and the data made completely public available in a database developed by our group available at: www.cochinealgenome.com.

OpenScience

About the Team:

vinicius-maracaja
Vinicius Maracaja-Coutinho (@viniciusmaracaja) was born in Paraíba, but currently lives in Chile. He has a PhD in Bioinformatics and a BSc degree in Biological Sciences. Founded Beagle Bioinformatics (Brazil and Chile) and is Assistant Professor at Universidad Mayor (Chile), where leads the Laboratory of Integrative Bioinformatics (www.integrativebioinformatics.me). Published 16 papers and presented 31 works in international scientific journals and meetings on the field of genomics and bioinformatics.

itacio
Itacio Padilha has a BSc in Biological Sciences from  Universidad Federal da Paraíba, and a PhD in Biotechnology from the same university, with an exchange research performed at Univesitat de Barcelona, España (2012-2013). Currently, he is a post-doctorate researcher leading the project “Protein Structural Bioinformatics: models, algorithms and biotech applications”. He is also the coordinator of the Graduate course “Biotechnology in Human Health”, from Faculdade Internacional de Paraíba (FPB).

 

Screen Shot 2016-04-14 at 1.04.05 PM
Demetrius de Araújo has a BSc in Pharmacy, a MSc in Biochemistry and Immunology, and a PhD in Biochemistry and Immunology. Between 1998-1999 he developed a post-doctorate research at  University of Leiscester, United Kingdom, under the supervision of Prof. Dr. P.R. Stanfield. Currently, he is Professor at the Department of Biotechnology, from Universidade Federal da Paraíba (UFPB), presidente del  CIBio/UFPB (CQB 0016/97), is the coordinator of the PhD in Biotechnology from UFPB and RENORBIO (Northeast Biotechnology Network), and is member of the board of directors of the Brazilian Biophysics Society.

Risks & Challenges:

Since this is a scientific project it is important to have in mind that the results obtained on the research can be inconclusive. However, we are sure that any additional information regarding to the identification of Cochineal genes will be of high importance to scientific community.

On the News:

onthenews2

 

7 Comments

  1. Profile photo of Orlando Ronaldy Santos Orlando Ronaldy Santos

    Bem, eu nasci no sertão e conheço bem a importância da palma pra população que sofre com a seca. Torço para que a meta seja alcançada e que o sequenciamento resulte em alguma alternativa viável para o problema. Parabéns pela iniciativa!

  2. Profile photo of Rubens Monte-Neto Rubens Monte-Neto

    Não apenas pela iniciativa de melhor conhecer uma praga para saber como combatê-la, mas apoio igualmente a ideia do crowdfunding. Sucesso nessa batalha!!!

  3. Profile photo of Felipy Rafael Pereira Felipy Rafael Pereira

    Essa é uma pesquisa essencial para encontrarmos alternativas eficientes para combater essa praga. Sempre digo que é papel tanto das Universidades, dos centros de pesquisa como dos agricultores investirem em pesquisas que busquem soluções para o homem do campo.
    Parabéns pela iniciativa e sempre conte comigo!

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  • 17 Backers

    PORTUGUÊS: Você receberá um agradecimento pessoal na sua timeline do Facebook ••• ENGLISH: You will receive a personal Thank You in your Facebook timeline ••• ESPAÑOL: Tu vas a recibir un Agradecimiento personalizado en el muro de tu Facebook

  • 31 Backers

    PORTUGUÊS: Seu nome aparecerá nos Agradecimentos na base de dados online que vamos gerar para o projeto, que ficará disponível no site: www.cochinealgenome.com. ••• ENGLISH: Your name will appear on the Acknowledgments in our final open source database at www.cochinealgenome.com. ••• ESPAÑOL: Aparecerá tu nombre en la sección de Agradecimientos en la base de datos que vamos generar para el proyecto, que quedará disponible en: www.cochinealgenome.com.

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    PORTUGUÊS: Você receberá a recompensa acima, além do sticker digital: "Faço parte do projeto genoma da cochonilha". ••• ENGLISH: You will receive the above-mentioned Reward, plus a digital sticker: "I am part of the Cochineal genome project". ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además del sticker digital: "Soy parte del proyecto genoma de la cochinilla".

  • 9 Backers

    PORTUGUÊS: Você receberá as recompensas acima, além de uma ilustração digital contendo todos os genes identificados no genoma da cochonilha. A ilustração estará disponível depois das análises do genoma. ••• ENGLISH: You will receive the above-mentioned Rewards, plus a digital illustration with all genes identified on the Cochineal genome. Note that this illustration will be made available after the genome analizys. ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además de una ilustración digital con todos los genes identificados en el genoma de la cochinilla. La ilustración estará disponible después de los análisis de los datos genómicos.

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    PORTUGUÊS: Você receberá as recompensas acima, além de participar de uma reunião virtual (por Skype) com a nossa equipe ••• ENGLISH: You will receive the above-mentioned Rewards, plus a Skype meeting with our team. ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además de participar de una reunión virtual (por Skype) con nuestro equipo.

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    PORTUGUÊS: Você receberá as recompensas acima, além de ter seu nome (ou o da sua empresa) listado nos Agradecimentos de todas as publicações científicas geradas com este projeto. ••• ENGLISH: You will receive all above-mentioned Rewards, plus your name (or your company's name) on the Acknowledgements of all publications generated by this research. ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además de tener tu nombre (o de tu empresa) listado en todas las publicaciones que salgan de este proyecto de investigación.

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    PORTUGUÊS: Você receberá as recompensas acima, além de uma visita para conhecer o Laboratório de Bioinformática Integrativa (www.integrativebioinformatics.me) em Santiago (Chile). Custos de viagem não incluídos. ••• ENGLISH: You will receive the above-mentioned Rewards, plus a visit to the Laboratory of Integrative Bioinformatics (www.integrativebioinformatics.me), in Santiago (Chile). Travel costs not included. ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además de una visita para conocer el Laboratório de Bioinformática Integrativa (www.integrativebioinformatics.me) en Santiago (Chile). Costos del viaje no incluídos.

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    PORTUGUÊS: Você receberá as recompensas acima listadas, além de uma viagem guiada à região do Cariri Paraibano,Paraíba, Brasil (hospedagem incluída em uma fazenda local, custos de viagem não incluídos) ••• ENGLISH: You will receive all above-mentioned Rewards, plus a guided visit to the Cariri Region in Paraíba, Brasil (housing provided for free in a local farm, travel costs not included). ••• ESPAÑOL: Vas a recibir las recompensas mencionadas arriba, además de una visita guiada en la región del Cariri Paraibano, Brasil (alojamiento incluído en una hacienda local, costos de viaje no incluídos).