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

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

UniProt: the universal protein knowledgebase

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Dinoflagellates, a Unique Lineage for Retrogene Research

(2018) Bo Song et al.   Frontiers in Microbiology

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution

(2017) Bo Song et al.   Genome Biology and Evolution

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes

(2017) Daniel Vitales et al.   PLANT SYSTEMATICS AND EVOLUTION

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

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Expansion of the Gene Ontology knowledgebase and resources

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Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

(2016) Shifeng Cheng et al.   PLANT JOURNAL

Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

(2016) Eunyoung Seo et al.   Frontiers in Plant Science

Extensive Families of miRNAs andPHASLoci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants

(2015) Rui Xia et al.   MOLECULAR BIOLOGY AND EVOLUTION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

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

(2014) Hideki Hirakawa et al.   DNA RESEARCH

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

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

(2014) Seungill Kim et al.   NATURE GENETICS

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

(2014) Laura Pascual et al.   PLANT BIOTECHNOLOGY JOURNAL

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 demographic response to Holocene climate change in the Sahara

(2014) Katie Manning et al.   QUATERNARY SCIENCE REVIEWS

Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes

(2014) Mariola Plazas et al.   Frontiers in Plant Science

Informed and automated k-mer size selection for genome assembly

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(2013) W. He et al.   GENETICS AND MOLECULAR RESEARCH

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(2012) Limin Fu et al.   BIOINFORMATICS

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

(2012) Kevin Stoffel et al.   BMC GENOMICS

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

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

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Genetic diversity among accessions of Solanum aethiopicum L. groups based on morpho-agronomic traits

(2012) O. T. Adeniji et al.   Plant Genetic Resources-Characterization and Utilization

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

(2012) Ruibang Luo et al.   GigaScience

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny

(2011) Milind B. Ratnaparkhe et al.   NEW PHYTOLOGIST

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

(2011) Jia-Xing Yue et al.   NEW PHYTOLOGIST

The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis

(2011) A. Suttangkakul et al.   PLANT CELL

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Characterization of Health-Related Compounds in Eggplant (Solanum melongenaL.) Lines Derived from Introgression of Allied Species

(2010) Giuseppe Mennella et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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(2009) M. D. Robinson et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Inheritance of Fusarium wilt resistance introgressed from Solanum aethiopicum Gilo and Aculeatum groups into cultivated eggplant (S. melongena) and development of associated PCR-based markers

(2008) Laura Toppino et al.   MOLECULAR BREEDING

Transgenic Arabidopsis Plants Expressing the Type 1 Inositol 5-Phosphatase Exhibit Increased Drought Tolerance and Altered Abscisic Acid Signaling

(2008) I. Y. Perera et al.   PLANT CELL