Using genomic repeats for phylogenomics: a case study in wild tomatoes (SolanumsectionLycopersicon: Solanaceae)

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Genomic Repeat Abundances Contain Phylogenetic Signal

(2014) S. Dodsworth et al.   SYSTEMATIC BIOLOGY

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy

(2013) Julien Haran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-Generation Museomics Disentangles One of the Largest Primate Radiations

(2013) Katerina Guschanski et al.   SYSTEMATIC BIOLOGY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

(2012) Wambui Njuguna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chromosome evolution in Solanum traced by cross-species BAC-FISH

(2012) Dóra Szinay et al.   NEW PHYTOLOGIST

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Chromosomal rearrangements between tomato and Solanum chilense hamper mapping and breeding of the TYLCV resistance gene Ty-1

(2011) Maarten G. Verlaan et al.   PLANT JOURNAL

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

FISH Applications for Genomics and Plant Breeding Strategies in Tomato and Other Solanaceous Crops

(2010) D. Szinay et al.   CYTOGENETIC AND GENOME RESEARCH

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

(2009) Flor Rodriguez et al.   BMC EVOLUTIONARY BIOLOGY

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Cross-Species Bacterial Artificial Chromosome–Fluorescence in Situ Hybridization Painting of the Tomato and Potato Chromosome 6 Reveals Undescribed Chromosomal Rearrangements

(2008) Xiaomin Tang et al.   GENETICS

The Use of Mean Instead of Smallest Interspecific Distances Exaggerates the Size of the “Barcoding Gap” and Leads to Misidentification

(2008) Rudolf Meier et al.   SYSTEMATIC BIOLOGY