All biological disciplines that depend on DNA sequence data have been fundamentally changed in the last few years, driven by the development and emergence of next-generation sequenc-

American Journal of Botany 99(2): 175–185, 2012; http://www.amjbot. org/ © 2012 Botanical Society of America All biological disciplines that depend on DNA sequence data have been fundamentally changed in the last few years, driven by the development and emergence of next-generation sequencing (NGS) technologies. Our knowledge of biology, particularly genomics, has grown exponentially. NGS methods have increased capabilities far beyond that of traditional Sanger sequencing ( Sanger et al., 1977 ), allowing millions of bases to be sequenced in one round at a fraction of the cost. As the costs and capabilities of these technologies continue to improve, whole new fi elds of study are being opened, allowing us to analyze a variety of data sets and approach questions never possible before. Improved sequencing is accompanied by many challenges as well as new developments. NGS technologies create a vast amount of data, presenting many problems to computational biologists, bioinformaticians, and end-users endeavoring to assemble and analyze NGS data in novel ways. A comprehensive discussion of these challenges is outside the scope of this review, but several papers in this issue address some of these issues and possible strategies for dealing with them (e.g., Cronn et al., 2012 ; Grover et al., 2012 ; Ilut et al., 2012 ; Kvam et al., 2012 ). Furthermore, these advancements have led to the requirement by most granting agencies and peer-reviewed journals that DNA sequence and other data are made publicly available online. This requirement has thus created the need for the development of databases to house and allow public access to NGS data (see McCouch et al., 2012 , in this issue) as well as a sustained commitment to fund and maintain such resources. One of us (D. Spooner) received his degree in prior rounds of “ next-generation ” techniques (e.g., fl avonoid chemistry and isozymes for systematic studies) and has seen many techniques develop since then (such as DNA restriction site phylogenies, Sanger sequencing, molecular marker developments). In the early stages of development, NGS was initially used by researchers such as plant breeders, working with model organisms of economic importance and backed by decades of research compiled within large genetic and genomic resources. However, techniques are rapidly improving and comparative sequences are accumulating and becoming suffi cient to act as reference genomes for assembly, thus allowing any organism to become a “ model ” organism. These and previous “ next-generation ” advancements only reinforce the need to continuously keep current in emerging techniques that expand our capabilities and possible avenues of research. This issue addresses recent advancements in NGS techniques and presents studies that point the way to entering this exciting fi eld. Here we briefl y review the various NGS methods currently on the market or under development and summarize the 19 papers presented in this special issue wherein a number of research studies illustrate how NGS techniques can be employed to address signifi cant and novel questions in plant biology.