PMID- 33469716
OWN - NLM
STAT- MEDLINE
DCOM- 20210225
LR  - 20210225
IS  - 1617-4623 (Electronic)
IS  - 1617-4623 (Linking)
VI  - 296
IP  - 2
DP  - 2021 Mar
TI  - Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters 
      impact biological results?
PG  - 457-471
LID - 10.1007/s00438-020-01756-9 [doi]
AB  - Next-generation sequencing technologies have opened a new era of research in 
      population genetics. Following these new sequencing opportunities, the use of 
      restriction enzyme-based genotyping techniques, such as restriction 
      site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing 
      (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to 
      SNP calling, the laboratory and bioinformatic parameters of enzyme-based 
      techniques have been investigated in the literature. However, the impact of those 
      parameters on downstream analyses and biological results remains less documented. 
      In this study, we investigated the effects of sevral pre- and post-sequencing 
      settings on ddRAD-seq results for two biological systems: a complex of butterfly 
      species (Coenonympha sp.) and several populations of common beech (Fagus 
      sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA 
      quantity, number of PCR cycles during library preparation) have a significant 
      impact on the number of recovered reads and SNPs, on the number of unique alleles 
      and on individual heterozygosity. In the same way, we found that post-sequencing 
      settings (i.e., clustering and minimum coverage thresholds) influenced loci 
      reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., 
      number of SNPs; heterozygosity) but had only a marginal impact on downstream 
      analyses (e.g., measure of genetic differentiation, estimation of individual 
      admixture, and demographic inferences). In addition, replication analyses 
      confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study 
      assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing 
      protocols, and illustrates its robustness when studying population genetics.
FAU - Cumer, Tristan
AU  - Cumer T
AUID- ORCID: 0000-0002-0276-7462
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
AD  - Department of Ecology and Evolution, UNIL-Sorge, University of Lausanne, 1015, 
      Biophore, Lausanne, Switzerland.
FAU - Pouchon, Charles
AU  - Pouchon C
AUID- ORCID: 0000-0001-7766-3732
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
FAU - Boyer, Frederic
AU  - Boyer F
AUID- ORCID: 0000-0003-0021-9590
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
FAU - Yannic, Glenn
AU  - Yannic G
AUID- ORCID: 0000-0002-6477-2312
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
FAU - Rioux, Delphine
AU  - Rioux D
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
FAU - Bonin, Aurelie
AU  - Bonin A
AUID- ORCID: 0000-0001-7800-8609
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France.
FAU - Capblancq, Thibaut
AU  - Capblancq T
AUID- ORCID: 0000-0001-5024-1302
AD  - Laboratoire D'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont 
      Blanc, CNRS, 38000, Grenoble, France. thibaut.capblancq@gmail.com.
AD  - Department of Plant Biology, University of Vermont, Burlington, VT, USA. 
      thibaut.capblancq@gmail.com.
LA  - eng
GR  - ANR-15-CE02-0004/ANR project APPATS/
GR  - ANR10 LABX56/Labex OSUG@2020/
GR  - CPER0713 CIRA/Auvergne-Rhone-Alpes region/
PT  - Journal Article
DEP - 20210120
PL  - Germany
TA  - Mol Genet Genomics
JT  - Molecular genetics and genomics : MGG
JID - 101093320
RN  - EC 3.1.21.- (DNA Restriction Enzymes)
SB  - IM
MH  - Alleles
MH  - Animals
MH  - Butterflies/*genetics
MH  - Computational Biology/methods
MH  - DNA Restriction Enzymes/metabolism
MH  - Fagus/*genetics
MH  - Genetics, Population
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Polymorphism, Single Nucleotide
MH  - Reproducibility of Results
MH  - Sequence Analysis, DNA/*methods
OTO - NOTNLM
OT  - Bioinformatics
OT  - Laboratory protocol
OT  - Molecular biology
OT  - Next-generation sequencing
EDAT- 2021/01/21 06:00
MHDA- 2021/02/26 06:00
CRDT- 2021/01/20 05:56
PHST- 2020/07/10 00:00 [received]
PHST- 2020/12/14 00:00 [accepted]
PHST- 2021/01/21 06:00 [pubmed]
PHST- 2021/02/26 06:00 [medline]
PHST- 2021/01/20 05:56 [entrez]
AID - 10.1007/s00438-020-01756-9 [pii]
AID - 10.1007/s00438-020-01756-9 [doi]
PST - ppublish
SO  - Mol Genet Genomics. 2021 Mar;296(2):457-471. doi: 10.1007/s00438-020-01756-9. 
      Epub 2021 Jan 20.