Difference between revisions of "Team:Valencia UPV/Software"
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| − | <section><div class="container-fluid"><div class="row"><div class="col-md-2 col-sm-3"><div class="side-nav margin-bottom-60 margin-top-30"><div class="side-nav-head"><button class="fa fa-bars"></button><h4>Index</h4></div><ul class="list-group list-group-bordered list-group-noicon uppercase"><li class="list-group-item"><a href="https://2016.igem.org/Team:Valencia_UPV/Software#DATABASE_id"><span class="size-11 text-muted pull-right"></span>DATA BASE</a></li><li class="list-group-item"><a href="https://2016.igem.org/Team:Valencia_UPV/Software#Databaseexample_id"><span class="size-11 text-muted pull-right"></span>Database example</a></li></ul></div></div><div class="col-md-10 col-sm-9"><div class="blog-post-item" id="DATABASE_id"><h3>DATA BASE</h3><p><br>Often, gene related information is available on the Internet, but people don’t always know where to look or how to search efficiently, and almost every time it is so difficult to interpret because it is not clear the function of these genes. Editing them usually leads to non desired modification. Plant proteins usually are involved in many metabolic processes simultaneously, so modifications in a particular protein could lead in a non viable plant. In other cases, those modifications lead to a fruitless variety, which many times has not an agricultural benefit. So that, many times is so difficult to know which gene a plant breeder must edit despite he knows what phenotypic trait he wants to obtain. <br><br>In HYPE-IT, we have worked hard looking for genes which knockout leads to an interesting phenotypic trait. Scientific articles web pages are full of papers where gene functions are identified, but not always are identified by knocking them out. We have only selected those articles where they have done the gene silencing, either by RNAi mediated silencing or by CRISPR/Cas9 editing, and they obtained a viable fruited plants. This allow us to avoid transgenesis because we don’t need to insert exogenous genes to obtain an enhanced plant variety. <br>Our database gather more than 20 different genes, which knockout leads to many different improved characteristics. All these genes are well referenced, so has been demonstrated plant viability in all the cases. However, there are many proteins that are homologous between them, so we can admit that they have the same function in other plant species. After doing Blastp exams, we finally obtained more than 200 targeting genes. This is a huge Database with a high interest for plant breeders and seedbeds. <br><br>Some gene examples of our Database are:<br><br> | + | <section><div class="container-fluid"><div class="row"><div class="col-md-2 col-sm-3"><div class="side-nav margin-bottom-60 margin-top-30"><div class="side-nav-head"><button class="fa fa-bars"></button><h4>Index</h4></div><ul class="list-group list-group-bordered list-group-noicon uppercase"><li class="list-group-item"><a href="https://2016.igem.org/Team:Valencia_UPV/Software#DATABASE_id"><span class="size-11 text-muted pull-right"></span>DATA BASE</a></li><li class="list-group-item"><a href="https://2016.igem.org/Team:Valencia_UPV/Software#Databaseexample_id"><span class="size-11 text-muted pull-right"></span>Database example</a></li></ul></div></div><div class="col-md-10 col-sm-9"><div class="blog-post-item" id="DATABASE_id"><h3>DATA BASE</h3><p><br>Often, gene related information is available on the Internet, but people don’t always know where to look or how to search efficiently, and almost every time it is so difficult to interpret because it is not clear the function of these genes. Editing them usually leads to non desired modification. Plant proteins usually are involved in many metabolic processes simultaneously, so modifications in a particular protein could lead in a non viable plant. In other cases, those modifications lead to a fruitless variety, which many times has not an agricultural benefit. So that, many times is so difficult to know which gene a plant breeder must edit despite he knows what phenotypic trait he wants to obtain. <br><br>In HYPE-IT, we have worked hard looking for genes which knockout leads to an interesting phenotypic trait. Scientific articles web pages are full of papers where gene functions are identified, but not always are identified by knocking them out. We have only selected those articles where they have done the gene silencing, either by RNAi mediated silencing or by CRISPR/Cas9 editing, and they obtained a viable fruited plants. This allow us to avoid transgenesis because we don’t need to insert exogenous genes to obtain an enhanced plant variety. <br>Our database gather more than 20 different genes, which knockout leads to many different improved characteristics. All these genes are well referenced, so has been demonstrated plant viability in all the cases. However, there are many proteins that are homologous between them, so we can admit that they have the same function in other plant species. After doing Blastp exams, we finally obtained more than 200 targeting genes. This is a huge Database with a high interest for plant breeders and seedbeds. <br><br>Some gene examples of our Database are:<br><br></p><ul><li>Ga20 oxidase, that leads to a smaller phenotype in maize or rice. All the energy that the modified plants would have used growing up, they would harness it increasing their grain properties and production.</li><li>TFL (terminal flower), is a key regulator of delaying flowering and regulating plant growth. Its knockdown leads to more flowering varieties. </li><li>ACS4 is a protein involved in the route of ethylene synthesis. It catalyzes the synthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) from S-Adenosyl methionine. Its knockdown leads to andromonoecy varieties. </li></ul><p><br>HYPE-IT Database also include important gene related information, such as the name of the gene and the protein targeted, the paper we have based on or the NCBI accession number. It allows us to organise information in a structured way, in addition to have it interconnected with other kind of databases. Mixing our Database and Software, we are able to obtain the optimal gRNA to a specific HYPE-IT Database gene using the scoring system of our Software. The objective is to reduce steps that plant breeders should do if they wanted to enhance a plant variety giving them all sequences they should order to synthesize. <br><br>We are very glad to the result of our Database. If you want to access to it, you should sign in our external webpage, located inside HYPE-IT sofware application. <br><br><a href="http://hypeit.cloudno.de/">http://hypeit.cloudno.de/</a><br><br><br>We also include here our database in .xls for anyone who wants to check it:<br><br><br><a href="https://static.igem.org/mediawiki/2016/7/75/T--Valencia_UPV--DataBaseReviewed.xlsx">HYPE-IT Database.xlsx</a><br><br><br>As a sample of how our Database is:<br><br></p></div><div class="blog-post-item" id="Databaseexample_id"><h3>Database example</h3><p></p><div class="table-responsive" style="width:55%;overflow:inherit"><table class="table table-bordered table-striped"><tr><th>Common name</th><th>Species</th><th>Phenotypic trait</th><th>Gene Name</th><th>NCBI CDS Accession number</th><th>Protein</th></tr><tr><td>Apple</td><td>Malus domestica</td><td>delayed ripening</td><td>MdACS3</td><td>AB243060</td><td>1-aminocyclopropane-1-carboxylate synthase</td></tr><tr><td>Tomato</td><td>Solanum lycopersicum</td><td>delayed ripening</td><td>Solanum lycopersicum 1-aminocyclopropane-1-carboxylate synthase (ACS6), mRNA</td><td>NM_001247235.2</td><td>1-aminocyclopropane-1-carboxylate synthase</td></tr><tr><td>Strawberry</td><td>Fragaria × ananassa</td><td>Flavonoid biosynthesis</td><td>Fragaria chiloensis transcription factor (MYB1) mRNA, complete cds</td><td> GQ867222.1</td><td>A R2R3 MYB transcription factor</td></tr><tr><td>Tomato </td><td>Solanum lycopersicum </td><td>Increase of carotenoid and flavonoid levels</td><td>Solanum lycopersicum deetiolated1 homolog (Det1), mRNA</td><td> NM_001247219.2</td><td>light-mediated development protein DET1</td></tr><tr><td>Orange tree</td><td>Citrus sinensis</td><td>induced flowering</td><td>Citrus sinensis terminal flower (TFL), mRNA</td><td>NM_001288919.1</td><td>terminal flower (TFL)</td></tr><tr><td>Maize</td><td>Zea mays</td><td>semi-dwarf; more grain yield</td><td>Zea mays (LOC107521947), mRNA</td><td>NM_001321686.1</td><td>GA3 oxidase</td></tr><tr><td>Rice</td><td>Oryza sativa</td><td>Drought Tolerance</td><td>PREDICTED: Oryza sativa Japonica Group E3 ubiquitin-protein ligase SINAT5 (LOC4344172), mRNA.</td><td> XM_015789296</td><td>E3 ubiquitin-protein ligase SINAT5</td></tr><tr><td>coffee</td><td>Coffea arabica</td><td>decaffeinated plants</td><td>Coffea arabica CaMXMT1 mRNA for 7-methylxanthine N-methyltransferase, complete cds.</td><td>AB048794</td><td>RecName: Full=Monomethylxanthine methyltransferase 1; Short=CaMXMT1; AltName: Full=Theobromine synthase 1</td></tr><tr><td>cotton</td><td>Gossypium hirsutum</td><td> increased stearic acid content</td><td>G.hinsutum mRNA for stearoyl-acyl-carrier protein desaturase</td><td> X95988</td><td>delta 9 stearoyl-(acyl-carrier protein) desaturase (Gossypium hirsutum)</td></tr><tr><td>cotton</td><td>Gossypium hirsutum</td><td>increased oleic acid content</td><td>Gossypium hirsutum delta(12)-fatty-acid desaturase FAD2-like (LOC107934594), mRNA.</td><td>NM_001327381</td><td>delta(12)-fatty-acid desaturase FAD2-like (Gossypium hirsutum)</td></tr><tr><td>corn</td><td>Zea mays</td><td>higher levels of amylose</td><td>Zea mays amylose extender 1 (ae1), mRNA.</td><td>NM_001111846</td><td>1,4-α-glucan-branching enzyme 2, chloroplastic/amyloplastic precursor (Zea mays)</td></tr><tr><td>onion </td><td>Allium roylei</td><td>reduced levels of tear-inducing lachrymatory factor</td><td>Allium roylei lachrymatory factor synthase (LFS) gene, partial cds.</td><td> HQ738919</td><td> lachrymatory factor synthase, partial (Allium roylei)</td></tr><tr><td>tomato </td><td>Solanum lycopersicum</td><td>Parthenocarpic</td><td>Solanum lycopersicum chalcone synthase (CHS2) mRNA, complete cds.</td><td> HQ008773</td><td>chalcone synthase (Solanum lycopersicum)</td></tr></table></div><p><br></p></div></div></div></section> |
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Revision as of 00:08, 20 October 2016
Data Processing Software
DATA BASE
Often, gene related information is available on the Internet, but people don’t always know where to look or how to search efficiently, and almost every time it is so difficult to interpret because it is not clear the function of these genes. Editing them usually leads to non desired modification. Plant proteins usually are involved in many metabolic processes simultaneously, so modifications in a particular protein could lead in a non viable plant. In other cases, those modifications lead to a fruitless variety, which many times has not an agricultural benefit. So that, many times is so difficult to know which gene a plant breeder must edit despite he knows what phenotypic trait he wants to obtain.
In HYPE-IT, we have worked hard looking for genes which knockout leads to an interesting phenotypic trait. Scientific articles web pages are full of papers where gene functions are identified, but not always are identified by knocking them out. We have only selected those articles where they have done the gene silencing, either by RNAi mediated silencing or by CRISPR/Cas9 editing, and they obtained a viable fruited plants. This allow us to avoid transgenesis because we don’t need to insert exogenous genes to obtain an enhanced plant variety.
Our database gather more than 20 different genes, which knockout leads to many different improved characteristics. All these genes are well referenced, so has been demonstrated plant viability in all the cases. However, there are many proteins that are homologous between them, so we can admit that they have the same function in other plant species. After doing Blastp exams, we finally obtained more than 200 targeting genes. This is a huge Database with a high interest for plant breeders and seedbeds.
Some gene examples of our Database are:
- Ga20 oxidase, that leads to a smaller phenotype in maize or rice. All the energy that the modified plants would have used growing up, they would harness it increasing their grain properties and production.
- TFL (terminal flower), is a key regulator of delaying flowering and regulating plant growth. Its knockdown leads to more flowering varieties.
- ACS4 is a protein involved in the route of ethylene synthesis. It catalyzes the synthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) from S-Adenosyl methionine. Its knockdown leads to andromonoecy varieties.
HYPE-IT Database also include important gene related information, such as the name of the gene and the protein targeted, the paper we have based on or the NCBI accession number. It allows us to organise information in a structured way, in addition to have it interconnected with other kind of databases. Mixing our Database and Software, we are able to obtain the optimal gRNA to a specific HYPE-IT Database gene using the scoring system of our Software. The objective is to reduce steps that plant breeders should do if they wanted to enhance a plant variety giving them all sequences they should order to synthesize.
We are very glad to the result of our Database. If you want to access to it, you should sign in our external webpage, located inside HYPE-IT sofware application.
http://hypeit.cloudno.de/
We also include here our database in .xls for anyone who wants to check it:
HYPE-IT Database.xlsx
As a sample of how our Database is:
Database example
| Common name | Species | Phenotypic trait | Gene Name | NCBI CDS Accession number | Protein |
|---|---|---|---|---|---|
| Apple | Malus domestica | delayed ripening | MdACS3 | AB243060 | 1-aminocyclopropane-1-carboxylate synthase |
| Tomato | Solanum lycopersicum | delayed ripening | Solanum lycopersicum 1-aminocyclopropane-1-carboxylate synthase (ACS6), mRNA | NM_001247235.2 | 1-aminocyclopropane-1-carboxylate synthase |
| Strawberry | Fragaria × ananassa | Flavonoid biosynthesis | Fragaria chiloensis transcription factor (MYB1) mRNA, complete cds | GQ867222.1 | A R2R3 MYB transcription factor |
| Tomato | Solanum lycopersicum | Increase of carotenoid and flavonoid levels | Solanum lycopersicum deetiolated1 homolog (Det1), mRNA | NM_001247219.2 | light-mediated development protein DET1 |
| Orange tree | Citrus sinensis | induced flowering | Citrus sinensis terminal flower (TFL), mRNA | NM_001288919.1 | terminal flower (TFL) |
| Maize | Zea mays | semi-dwarf; more grain yield | Zea mays (LOC107521947), mRNA | NM_001321686.1 | GA3 oxidase |
| Rice | Oryza sativa | Drought Tolerance | PREDICTED: Oryza sativa Japonica Group E3 ubiquitin-protein ligase SINAT5 (LOC4344172), mRNA. | XM_015789296 | E3 ubiquitin-protein ligase SINAT5 |
| coffee | Coffea arabica | decaffeinated plants | Coffea arabica CaMXMT1 mRNA for 7-methylxanthine N-methyltransferase, complete cds. | AB048794 | RecName: Full=Monomethylxanthine methyltransferase 1; Short=CaMXMT1; AltName: Full=Theobromine synthase 1 |
| cotton | Gossypium hirsutum | increased stearic acid content | G.hinsutum mRNA for stearoyl-acyl-carrier protein desaturase | X95988 | delta 9 stearoyl-(acyl-carrier protein) desaturase (Gossypium hirsutum) |
| cotton | Gossypium hirsutum | increased oleic acid content | Gossypium hirsutum delta(12)-fatty-acid desaturase FAD2-like (LOC107934594), mRNA. | NM_001327381 | delta(12)-fatty-acid desaturase FAD2-like (Gossypium hirsutum) |
| corn | Zea mays | higher levels of amylose | Zea mays amylose extender 1 (ae1), mRNA. | NM_001111846 | 1,4-α-glucan-branching enzyme 2, chloroplastic/amyloplastic precursor (Zea mays) |
| onion | Allium roylei | reduced levels of tear-inducing lachrymatory factor | Allium roylei lachrymatory factor synthase (LFS) gene, partial cds. | HQ738919 | lachrymatory factor synthase, partial (Allium roylei) |
| tomato | Solanum lycopersicum | Parthenocarpic | Solanum lycopersicum chalcone synthase (CHS2) mRNA, complete cds. | HQ008773 | chalcone synthase (Solanum lycopersicum) |
