Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense , reveals residual heterozygosity

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

(2017) Satria A. Kautsar et al.   NUCLEIC ACIDS RESEARCH

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

Reinventing Potato as a Diploid Inbred Line–Based Crop

(2016) Shelley H. Jansky et al.   CROP SCIENCE

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

Genetic mapping with an inbred line-derived F2 population in potato

(2016) Jeffrey B. Endelman et al.   THEORETICAL AND APPLIED GENETICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

TheSolanum commersoniiGenome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

(2015) Riccardo Aversano et al.   PLANT CELL

Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history

(2015) Peter G. Vos et al.   THEORETICAL AND APPLIED GENETICS

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

(2014) Hideki Hirakawa et al.   DNA RESEARCH

M6: A Diploid Potato Inbred Line for Use in Breeding and Genetics Research

(2014) S. H. Jansky et al.   Journal of Plant Registrations

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

(2013) Sanjeev Kumar Sharma et al.   G3-Genes Genomes Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Single nucleotide polymorphism discovery in elite north american potato germplasm

(2011) John P Hamilton et al.   BMC GENOMICS

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Towards F1 Hybrid Seed Potato Breeding

(2011) Pim Lindhout et al.   POTATO RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE