TY - JOUR
T1 - Next-generation biology
T2 - sequencing and data analysis approaches for non-model organisms
AU - Rodrigues da Fonseca, Rute Andreia
AU - Albrechtsen, Anders
AU - Themudo, Goncalo Espregueira Cruz
AU - Ramos Madrigal, Jazmin
AU - Sibbesen, Jonas Andreas
AU - Sørensen, Lasse Maretty
AU - Zepeda Mendoza, Marie Lisandra
AU - Campos, Paula
AU - Heller, Rasmus
AU - Pereira, Ricardo
N1 - Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.
PY - 2016/12/1
Y1 - 2016/12/1
N2 - As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, a limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research in non-model organisms, they also demand unprecedented awareness from the researcher regarding the assumptions and limitations of each method. In this review we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing unconventional sample material, comparative and population genetic approaches that do not require fully assembled genomes, and advice on how to deal with low depth sequencing data.
AB - As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, a limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research in non-model organisms, they also demand unprecedented awareness from the researcher regarding the assumptions and limitations of each method. In this review we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing unconventional sample material, comparative and population genetic approaches that do not require fully assembled genomes, and advice on how to deal with low depth sequencing data.
U2 - 10.1016/j.margen.2016.04.012
DO - 10.1016/j.margen.2016.04.012
M3 - Journal article
C2 - 27184710
SN - 1874-7787
VL - 30
SP - 3
EP - 13
JO - Marine Genomics
JF - Marine Genomics
ER -