Ultra conserved elements as a time and cost efficient approach to understand geographical parthenogenesis and phylogenomics of nematodes

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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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