The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next‐generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select “model organisms”, is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.

Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum . We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: ( i ) putative diploids, ( ii ) putative tetraploids, and ( iii ) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri , S. juzepczukii , and S. curtilobum . In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: ( i ) S. tuberosum , with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); ( ii ) S. ajanhuiri (diploid); ( iii ) S. juzepczukii (triploid); and ( iv ) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature.

Solanum L. es uno de los géneros que posee una alta riqueza de especies dentro de la flora peruana y dentro de los Andes tropicales en general. Presentamos una lista revisada de 276 especies de Solanum para el Perú, de estas 253 son nativas, mientras que 23 son introducidas y/o cultivadas. Un total de 74 especies de Solanum (29% de las especies nativas) son endémicas de Perú. Además 58 especies se encuentran solamente en pequeñas poblaciones fuera del Perú, y estas especies están designadas aquí como casi endémicas para destacar el rol importante del Perú en la futura protección de estas especies. El pico de diversidad de especies es observado entre 2500 – 3000 m de elevación, pero la diversidad de especies endémicas es más alta entre 3000 – 3500 m. Cajamarca tiene el más alto número de especies (130 spp.) y de especies endémicas (29 spp.), incluso si se considera el efecto del área. Centros de diversidad de especies endémicas se localizan en las provincias de Cajamarca (Cajamarca), Huaraz y Carhuaz (Ancash), Canta y Huarochirí (Lima). Centros de endemismos secundarios con una alta concentración tanto de especies endémicas y de casi endémicas se encuentran en San Ignacio y Cutervo (Cajamarca), Santiago de Chuco (La Libertad), Oxapampa (Pasco), y Cusco (Cusco): Los actuales patrones de diversidad están altamente correlacionados con la densidad de colecciones, por lo que es necesario una mayor colecta en todas las regiones, especialmente en Arequipa, Ayacucho, Puno, Ancash, Huánuco, Amazonas y Cajamarca, donde se indican altos niveles de diversidad y endemismo de especies, pero de las cuales existen pocas colecciones.

Background: Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results: Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions: This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.