Second-generation nucleic-acid sequencing and bioarchaeology - Review

The nucleic-acid revolution started 31 years ago. The development of the second-generation sequencing (SGS) has allowed a higher throughput and lower price per sequenced base, opening the possibility to sequence ancient genomes, including epigenetics. The main SGS platforms are described in this review: i) Roche 454 Life Sciences, based on emulsion PCR (emPCR) and further pyrosequencing; ii) Illumina (bridge-amplification and subsequent reversible-terminator sequencing); iii) Life Technologies SOLiD (emPCR coupled with oligonucleotide ligation to interrogate DNA); and iv) Life Technologies Ion-Torrent-chip (emPCR, further using microchip pH-meters). Different ancient genomes (including viruses, microorganisms, plants and animals) have been sequenced. This has allowed to study the evolution of pathogens, domestication of microorganisms, plants and animals, paleodiets and paleoenvironments, including climate changes. Some hurdles and challenges must yet be overcome, but the steady technological advances in nucleic-acid isolation, sequencing and bioinformatics (together with higher computing power) promise a bright future for bioarchaeology in general, and paleogenomics in particular, allowing to analyze not just single genomes, but also to address ancient population genomics and evolution.Supported by “Ministerio de Economía y Competitividad” (MINECO grants AGL2010-17316 and BIO2011-15237-E) and “Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria” (MINECO and INIA RF2012-00002-C02-02); “Consejería de Agricultura y Pesca” (041/C/2007, 75/C/2009 and 56/C/2010), “Consejería de Economía, Innovación y Ciencia” (P11-AGR-7322 and P12-AGR-0482) and “Grupo PAI” (AGR-248) of “Junta de Andalucía”; and “Universidad de Córdoba” (“Ayuda a Grupos”), Spain.Peer reviewe