Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia

(2018) Pablo Muñoz-Rodríguez et al.   CURRENT BIOLOGY

Gene Pool Subdivision of East African Sweetpotato Parental Material

(2018) Maria C. David et al.   CROP SCIENCE

Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato

(2017) Gina M. Pham et al.   PLANT JOURNAL

Genome diversity of tuber-bearingSolanumuncovers complex evolutionary history and targets of domestication in the cultivated potato

(2017) Michael A. Hardigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tackling vitamin A deficiency with biofortified sweetpotato in sub-Saharan Africa

(2017) Jan W. Low et al.   Global Food Security-Agriculture Policy Economics and Environment

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don

(2015) H. Hirakawa et al.   DNA RESEARCH

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rphylip: an R interface for PHYLIP

(2014) Liam J. Revell et al.   Methods in Ecology and Evolution

Morphological and genetic differentiation and reproductive isolation among closely related taxa in the Ipomoea series Batatas

(2013) Tanya M. Duncan et al.   AMERICAN JOURNAL OF BOTANY

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Copy number variation in potato - an asexually propagated autotetraploid species

(2013) Marina Iovene et al.   PLANT JOURNAL

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Disentangling the Origins of Cultivated Sweet Potato (Ipomoea batatas (L.) Lam.)

(2013) Caroline Roullier et al.   PLoS One

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From the Cover: Cozzarelli Prize Winner: Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination

(2013) C. Roullier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Multiple biological functions of sporamin related to stress tolerance in sweet potato (Ipomoea batatas Lam)

(2012) Rajendran Senthilkumar et al.   BIOTECHNOLOGY ADVANCES

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Orange-fleshed sweetpotatoes for food, health and wealth in Uganda

(2011) Robert O. M. Mwanga et al.   International Journal of Agricultural Sustainability

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Novel interspecific hybridization between sweetpotato (Ipomoea batatas (L.) Lam.) and its two diploid wild relatives

(2009) Qinghe Cao et al.   EUPHYTICA

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Expression of class I knotted1-like homeobox genes in the storage roots of sweetpotato (Ipomoea batatas)

(2008) Masaru Tanaka et al.   JOURNAL OF PLANT PHYSIOLOGY

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE