Academic Journal
Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
| العنوان: | Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference |
|---|---|
| المؤلفون: | Mastretta-Yanes, Alicia, Arrigo, Nils, Álvarez, Nadir, Jorgensen, Tove H., Piñero, Daniel, Emerson, Brent C. |
| المساهمون: | Consejo Nacional de Ciencia y Tecnología (México) |
| بيانات النشر: | Wiley-Blackwell |
| سنة النشر: | 2015 |
| المجموعة: | Digital.CSIC (Consejo Superior de Investigaciones Científicas / Spanish National Research Council) |
| مصطلحات موضوعية: | De Novo Assembly, Optimization, RAD Sequencing, Replicates, Stacks, Error Rate |
| الوصف: | Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high‐altitude mountains in Mexico. ; This work has been supported by a CONACYT doctorate scholarship to AMY (213538), by a CONACYT Grant to DP (178245), by a SSE Rosemary Grant Student Research Award to AMY and by an SNSF Grant (PP00P3_144870) to N. Alvarez. ; Peer reviewed ; Peer Reviewed |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | unknown |
| تدمد: | 1755-098X |
| Relation: | Postprint; https://doi.org/10.1111/1755-0998.12291; Sí; e-issn: 1755-0998; Molecular Ecology Resources 15(1): 28-41 (2015); http://hdl.handle.net/10261/181064; http://dx.doi.org/10.13039/501100003141 |
| DOI: | 10.1111/1755-0998.12291 |
| DOI: | 10.13039/501100003141 |
| الاتاحة: | http://hdl.handle.net/10261/181064 https://doi.org/10.1111/1755-0998.12291 https://doi.org/10.13039/501100003141 |
| Rights: | open |
| رقم الانضمام: | edsbas.C1DF2040 |
| قاعدة البيانات: | BASE |
| تدمد: | 1755098X |
|---|---|
| DOI: | 10.1111/1755-0998.12291 |