Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becom...
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2018
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Online Access: | https://orbit.dtu.dk/en/publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 https://doi.org/10.1016/j.margen.2018.02.002 https://backend.orbit.dtu.dk/ws/files/190886068/Performance_and_precision_of_double_digestion_RAD_ddRAD_genotyping_in_large_multiplexed_datasets_of_marine_fish_species.pdf |
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ftdtupubl:oai:pure.atira.dk:publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 2024-09-15T18:40:01+00:00 Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species Maroso, F. Hillen, J E J Pardo, B. G. Gkagkavouzis, K. Coscia, I. Hermida, M. Franch, R. Hellemans, B. Van Houdt, J. Simionati, B. Taggart, J. B. Nielsen, Einar Eg Maes, G. Ciavaglia, S. A. Webster, L. M. I. Volckaert, F. A. M. Martinez, P. Bargelloni, L. Ogden, R. AquaTrace, Consortium 2018 application/pdf https://orbit.dtu.dk/en/publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 https://doi.org/10.1016/j.margen.2018.02.002 https://backend.orbit.dtu.dk/ws/files/190886068/Performance_and_precision_of_double_digestion_RAD_ddRAD_genotyping_in_large_multiplexed_datasets_of_marine_fish_species.pdf eng eng https://orbit.dtu.dk/en/publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 info:eu-repo/semantics/openAccess Maroso , F , Hillen , J E J , Pardo , B G , Gkagkavouzis , K , Coscia , I , Hermida , M , Franch , R , Hellemans , B , Van Houdt , J , Simionati , B , Taggart , J B , Nielsen , E E , Maes , G , Ciavaglia , S A , Webster , L M I , Volckaert , F A M , Martinez , P , Bargelloni , L , Ogden , R & AquaTrace , C 2018 , ' Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species ' , Marine Genomics , vol. 39 , pp. 64-72 . https://doi.org/10.1016/j.margen.2018.02.002 European sea bass GBS Gilthead sea bream Sequencing precision Turbot ddRAD /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water article 2018 ftdtupubl https://doi.org/10.1016/j.margen.2018.02.002 2024-08-05T23:48:29Z The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies. Article in Journal/Newspaper Turbot Technical University of Denmark: DTU Orbit Marine Genomics 39 64 72 |
institution |
Open Polar |
collection |
Technical University of Denmark: DTU Orbit |
op_collection_id |
ftdtupubl |
language |
English |
topic |
European sea bass GBS Gilthead sea bream Sequencing precision Turbot ddRAD /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
spellingShingle |
European sea bass GBS Gilthead sea bream Sequencing precision Turbot ddRAD /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water Maroso, F. Hillen, J E J Pardo, B. G. Gkagkavouzis, K. Coscia, I. Hermida, M. Franch, R. Hellemans, B. Van Houdt, J. Simionati, B. Taggart, J. B. Nielsen, Einar Eg Maes, G. Ciavaglia, S. A. Webster, L. M. I. Volckaert, F. A. M. Martinez, P. Bargelloni, L. Ogden, R. AquaTrace, Consortium Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
topic_facet |
European sea bass GBS Gilthead sea bream Sequencing precision Turbot ddRAD /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
description |
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies. |
format |
Article in Journal/Newspaper |
author |
Maroso, F. Hillen, J E J Pardo, B. G. Gkagkavouzis, K. Coscia, I. Hermida, M. Franch, R. Hellemans, B. Van Houdt, J. Simionati, B. Taggart, J. B. Nielsen, Einar Eg Maes, G. Ciavaglia, S. A. Webster, L. M. I. Volckaert, F. A. M. Martinez, P. Bargelloni, L. Ogden, R. AquaTrace, Consortium |
author_facet |
Maroso, F. Hillen, J E J Pardo, B. G. Gkagkavouzis, K. Coscia, I. Hermida, M. Franch, R. Hellemans, B. Van Houdt, J. Simionati, B. Taggart, J. B. Nielsen, Einar Eg Maes, G. Ciavaglia, S. A. Webster, L. M. I. Volckaert, F. A. M. Martinez, P. Bargelloni, L. Ogden, R. AquaTrace, Consortium |
author_sort |
Maroso, F. |
title |
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
title_short |
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
title_full |
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
title_fullStr |
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
title_full_unstemmed |
Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species |
title_sort |
performance and precision of double digestion rad (ddrad) genotyping in large multiplexed datasets of marine fish species |
publishDate |
2018 |
url |
https://orbit.dtu.dk/en/publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 https://doi.org/10.1016/j.margen.2018.02.002 https://backend.orbit.dtu.dk/ws/files/190886068/Performance_and_precision_of_double_digestion_RAD_ddRAD_genotyping_in_large_multiplexed_datasets_of_marine_fish_species.pdf |
genre |
Turbot |
genre_facet |
Turbot |
op_source |
Maroso , F , Hillen , J E J , Pardo , B G , Gkagkavouzis , K , Coscia , I , Hermida , M , Franch , R , Hellemans , B , Van Houdt , J , Simionati , B , Taggart , J B , Nielsen , E E , Maes , G , Ciavaglia , S A , Webster , L M I , Volckaert , F A M , Martinez , P , Bargelloni , L , Ogden , R & AquaTrace , C 2018 , ' Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species ' , Marine Genomics , vol. 39 , pp. 64-72 . https://doi.org/10.1016/j.margen.2018.02.002 |
op_relation |
https://orbit.dtu.dk/en/publications/1ec3ec71-0196-43f0-be72-3fa7ad65e2d4 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1016/j.margen.2018.02.002 |
container_title |
Marine Genomics |
container_volume |
39 |
container_start_page |
64 |
op_container_end_page |
72 |
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1810484340736393216 |