next-generation sequencing

Cynthia Steiner, Aryn Wilder, Debra Shier and Natalie Calatayud, San Diego Zoo Institute of Conservation Research

Among the main roles of conservation management is to mitigate the negative effect of anthropogenic activities in nature by ensuring the persistence of biodiversity and species in the wild. Conservation geneticists have recently developed a new toolbox of genomic methods to address the management of species in-situ and ex-situ. Among these approaches, the reduce representation or ddRADseq method allows to sample a fraction of the genome-wide genetic variation to estimate population summary statistics and individuals’ relationships for breeding management. The study of the southern mountain yellow-legged frog, an endemic and critically endangered amphibian species from southern California provides importance lessons about the use of ddRADseq in species with large genome size, in terms of quality/quantity of DNA samples required for generating genomic libraries, quality control of restriction enzymes chosen, optimization of parameters in the STACK pipeline for data analysis and selection of criteria for filtering genetic variants.

Date Recorded: 
Tuesday, September 10, 2019

Dr. Sally M Chambers, Marie Selby Botanical Gardens

Next generation sequencing technologies have rapidly developed over the past decade, providing new avenues for scientists working on non-model organisms to study patterns at the genome level. Techniques can be used to drastically simplify a complex genome and multiplex samples, which help make these sequencing platforms more cost effective than traditional methods when standardized by the amount of data generated. However, a number of factors need to be taken into account when developing a next-generation sequencing project, including genome size and complexity. Ferns are well known for having large and complex genomes, as many lineages are characterized by reticulate evolution. This produces species complexes that contain multiple hybrid individuals. Based on recent experiences in developing a study to resolve relationships within a species complex of North American Dryopteris, the applicability of double-digest RAD sequencing proved difficult. Lessons learned from this experience will be shared in order to assist others that would like to apply RADseq technologies to taxa with large or complex genomes.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019