Briscoe, Andrew G., Goodacre, Sarah, Masta, Susan E., Taylor, Martin I., Arnedo, Miquel A., Penney, David, Kenny, John, Creer, Simon and Goodacre, Sara (2013) Data from: Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). [Data Collection]
Description
The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods.
| Keywords: | Dryad,Cithaeron Praedonius,Anyphaena accentuata,Zelotes apricorum,Grammostola rosea,Segestria senoculata,Agalenatea redii,Malthonica silvestris,Gorgyrella sp.,Araneus diadematus,Salticus scenicus,mitogenomics,Selenops annulatus,Dysdera erythrina,Messapus martini,Pholcus phalangioides,Linyphiidae sp.,Theridiosoma gemmosum,Micrommata virescens,Argyroneta aquatica,long-range PCR amplification,Next-generation sequencing,Pardosa nigriceps,Amaurobius similis,Philodromus dispar,Xysticus audax,Meta menardi,Psalmopoeus cambridgei,Miagrammopes sp.,Eupalaestrus campestratus,Pisaura mirabilis,Phrurolithus festivus,Anahita sp.,Deinopis sp.,Clunbiona terrestris,Dictyna latens,Stegodyphus sp., |
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| Divisions: | Faculty of Health and Life Sciences |
| Depositing User: | Data Catalogue Admin |
| Date Deposited: | 23 Nov 2022 15:40 |
| Last Modified: | 23 Nov 2022 15:40 |
| DOI: | 10.5061/dryad.8dd3n |
| Original Record Link: | https://datadryad.org/stash/share/7AjFLM3tE4-uiKczqsMPCTTMde2Nr6iZHaByNkLfBUQ |
| URI: | https://datacat.liverpool.ac.uk/id/eprint/1907 |
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