A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family

(2020) Meng-Yao Li et al.   Horticulture Research

Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant

(2020) Qingzhen Wei et al.   Frontiers in Genetics

Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence

(2019) Anna Page et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species

(2019) Deling Sun et al.   Horticulture Research

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

(2019) Bo Song et al.   GigaScience

A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution

(2019) Lorenzo Barchi et al.   Scientific Reports

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

(2019) Dongmei Yin et al.   Advanced Science

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

QTL analysis reveals new eggplant loci involved in resistance to fungal wilts

(2018) Lorenzo Barchi et al.   EUPHYTICA

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

(2017) En-Hua Xia et al.   Molecular Plant

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant (Solanum melongena)

(2015) Koji Miyatake et al.   THEORETICAL AND APPLIED GENETICS

Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant

(2015) Ezio Portis et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

(2014) Fabio Cericola et al.   BMC GENOMICS

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

(2014) Hideki Hirakawa et al.   DNA RESEARCH

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

(2014) Amy Frary et al.   EUPHYTICA

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

(2014) Seungill Kim et al.   NATURE GENETICS

QTL Mapping in Eggplant Reveals Clusters of Yield-Related Loci and Orthology with the Tomato Genome

(2014) Ezio Portis et al.   PLoS One

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Characterization of interspecific hybrids and first backcross generations from crosses between two cultivated eggplants (Solanum melongena and S. aethiopicum Kumba group) and implications for eggplant breeding

(2012) Jaime Prohens et al.   EUPHYTICA

Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication

(2012) Rachel S. Meyer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation

(2012) Lorenzo Barchi et al.   PLoS One

Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets

(2012) Hiroyuki Fukuoka et al.   THEORETICAL AND APPLIED GENETICS

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Eggplant relatives as sources of variation for developing new rootstocks: Effects of grafting on eggplant yield and fruit apparent quality and composition

(2011) Carmina Gisbert et al.   SCIENTIA HORTICULTURAE

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

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY