Assessing a novel sequencing-based approach for population genomics in non-model species

Abstract

An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species (2020), bioRxiv, 10.1101/583534, ver. 7 peer-reviewed and recommended by Peer Community in Genomics. https://doi. Cite this recommendation as: Thomas Derrien and Sebastian Ramos-Onsins (2020) Assessing a novel sequencing-based approach for population genomics in non-model species. Peer Community in Genomics, 100002. 10.24072/pci.genomics.100002 Developing new sequencing and bioinformatic strategies for non-model species is of great interest in many applications, such as phylogenetic studies of diverse related species, but also for studies in population genomics, where a relatively large number of individuals is necessary. Different approaches have been developed and used in these last two decades, such as RAD-Seq (e.g., Miller et al. 2007), exome sequencing (e.g., Teer and Mullikin 2010) and other genome reduced representation methods that avoid the use of a good reference and well annotated genome (reviewed at Davey et al. 2011). However, population genomics studies require the analysis of numerous individuals, which makes the studies still expensive. Pooling samples was thought as an inexpensive strategy to obtain estimates of variability and other related to the frequency spectrum, thus allowing the study of variability at population level (e.g., Van Tassell et al. 2008), although the major drawback was the loss of information related to the linkage of the variants. In addition, population analysis using all these sequencing strategies require statistical and empirical validations that are not always fully performed. A number of studies aiming to obtain unbiased estimates of variability using reduced representation libraries and/or with pooled data have been performed (e.g., Futschik and Schlötterer