2020
DOI: 10.1101/2020.04.03.024331
|View full text |Cite
Preprint
|
Sign up to set email alerts
|

Achieving high-quality ddRAD-like reference catalogs for non-model species: the power of overlapping paired-end reads

Abstract: Reduced representation libraries present an opportunity to perform large scale studies on non-model species without the need for a reference genome. Methods that use restriction enzymes and fragment size selection to help obtain the desired number of loci -such as ddRAD -are highly flexible and therefore suitable to different types of studies. However, a number of technical issues are not approachable without a reference genome, such as size selection reproducibility across samples and coverage across fragment… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

0
9
0

Year Published

2020
2020
2024
2024

Publication Types

Select...
4
3

Relationship

5
2

Authors

Journals

citations
Cited by 12 publications
(9 citation statements)
references
References 70 publications
0
9
0
Order By: Relevance
“…The initial selection of nDNA markers was performed using a reduced genomic dataset produced via ddRAD. As a preliminary analysis to help establishing a standardized ddRAD protocol for sea turtles (Driller et al 2020), one individual of each parental species ( E. imbricata and C. caretta) and one F1 Ei × Cc hybrid individual were used for ddRAD library construction. The sequencing library was generated by digesting the genomic DNA using the restriction enzymes Nde I and Mlu CI with subsequent ligation of Illumina adapters followed by a 10-cycle Polymerase Chain Reaction (PCR) for completeness of sequencing adapters, as described in Peterson et al (2012).…”
Section: Methodsmentioning
confidence: 99%
“…The initial selection of nDNA markers was performed using a reduced genomic dataset produced via ddRAD. As a preliminary analysis to help establishing a standardized ddRAD protocol for sea turtles (Driller et al 2020), one individual of each parental species ( E. imbricata and C. caretta) and one F1 Ei × Cc hybrid individual were used for ddRAD library construction. The sequencing library was generated by digesting the genomic DNA using the restriction enzymes Nde I and Mlu CI with subsequent ligation of Illumina adapters followed by a 10-cycle Polymerase Chain Reaction (PCR) for completeness of sequencing adapters, as described in Peterson et al (2012).…”
Section: Methodsmentioning
confidence: 99%
“…The initial selection of nDNA markers was performed using a reduced genomic dataset produced via ddRAD. As a preliminary analysis to help establishing a standardized ddRAD protocol for sea turtles (Driller et al 2020), one individual of each parental species (E. imbricata . CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”
Section: Discovery and Standardization Of Nuclear Markersmentioning
confidence: 99%
“…2016). First, because the genome of the aquatic warbler is not yet available, we constructed a reference genomic library according to the Reduced-Representation Single-Copy Orthologs (R2SCOs) method, following Driller et al . (2021), with modifications (see below).…”
Section: Methodsmentioning
confidence: 99%