Ultra conserved elements as a time and cost efficient approach to understand geographical parthenogenesis and phylogenomics of nematodes
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Identification
| Title: | Main Title: Ultra conserved elements as a time and cost efficient approach to understand geographical parthenogenesis and phylogenomics of nematodes |
| Description: | Other: Bait design to target ultra conserved elements (UCEs) on nematodes belonging to the Panagrolaimoidea superfamily. These highly conserved regions in genomes are shared between evolutionary distant taxa and can provide insights on population genomics of differential reproducing nematodes as well as reconstruct the phylogenetic relationship between nematodes distributed all over the world, including those that have already been isolated from the Atacama Desert and are currently kept as laboratory cultures. |
Responsible Party
| Creators: | Laura Villegas (Author), Laura Pettrich (Author), Oleksandr Holovachov (Author), Ann-Marie Waldvogel (Principal Investigator), Philipp Schiffer (Principal Investigator) |
| Publisher: | CRC1211 Database (CRC1211DB) |
| Publication Year: | 2023 |
Topic
| CRC1211 Topic: | Biology |
| Related Subproject: | B8 |
| Subjects: | Keywords: Biodiversity, Molecular Biology |
| Geogr. Information Topic: | Biota |
File Details
| Filename: | baitset_Panagrolaimus1-v1-master-probe-list-DUPE-SCREENED.txt |
| Data Type: | Dataset - Bait set targetting UCEs |
| File Size: | 6.5 MB |
| Date: | Updated: 23.05.2023 |
| Mime Type: | text/plain |
| Data Format: | OTHER |
| Language: | English |
| Status: | In Process |
Constraints
| Download Permission: | Only Project Members |
| General Access and Use Conditions: | According to the CRC1211DB data policy agreement. |
| Access Limitations: | According to the CRC1211DB data policy agreement. |
| Licence: | [CRC1211DB] Data policy agreement |
Geographic
Specific Information - Data
| Temporal Extent: | 02.03.2022 - 31.05.2023 |
| Lineage: | Baits have been designed using existing genomes available through NCBI and newly assembled genomes generated by the AG Schiffer and AG Waldvogel from both desert nematodes and isolates from other locations. The design was performed using Phyluce (v 1.7.2) and baits were validated in-silico using Phyluce (v. 1.7.3) (https://doi.org/10.1093/bioinformatics/btv646). The set of baits was further on assessed by the oligo provider company prior to synthesis. Further experiments in the wet lab will follow. |
| Subtype: | Natural Science Data |
Metadata Details
| Metadata Creator: | Laura Villegas |
| Metadata Created: | 31.08.2023 |
| Metadata Last Updated: | 31.08.2023 |
| Subproject: | B8 |
| Funding Phase: | 2 |
| Metadata Language: | English |
| Metadata Version: | V50 |
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Dataset Statistics
| Page Visits: | 33 |
| Metadata Downloads: | 0 |
| Dataset Downloads: | 0 |
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