Wolfberry genomes and the evolution of Lycium (Solanaceae)

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Haplotype-resolved genome analyses of a heterozygous diploid potato

(2020) Qian Zhou et al.   NATURE GENETICS

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

(2020) Xin Wang et al.   Nature Communications

Functional MYB transcription factor encoding gene AN2 is associated with anthocyanin biosynthesis in Lycium ruthenicum Murray

(2019) Yuan Zong et al.   BMC PLANT BIOLOGY

Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum

(2019) Yunshu Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Systematic Analysis of MYB Family Genes in Potato and Their Multiple Roles in Development and Stress Responses

(2019) Xiaoxu Li et al.   Biomolecules

Comparison and multivariate statistical analysis of anthocyanin composition in Lycium ruthenicum Murray from different regions to trace geographical origins: The case of China

(2018) Zichao Wang et al.   FOOD CHEMISTRY

Physiological response of four wolfberry ( Lycium Linn.) species under drought stress

(2018) Jian-hua ZHAO et al.   Journal of Integrative Agriculture

Arabinogalactan proteins and their sugar chains: functions in plant reproduction, research methods, and biosynthesis

(2018) Shihao Su et al.   Plant Reproduction

A pectin from fruits of Lycium barbarum L. decreases β-amyloid peptide production through modulating APP processing

(2018) Lishuang Zhou et al.   CARBOHYDRATE POLYMERS

OUP accepted manuscript

(2018)   PLANT AND CELL PHYSIOLOGY

wgd—simple command line tools for the analysis of ancient whole-genome duplications

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

Genome-wide survey of potato MADS-box genes reveals that StMADS1 and StMADS13 are putative downstream targets of tuberigen StSP6A

(2018) Huhu Gao et al.   BMC GENOMICS

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

(2018) Shan Wu et al.   Nature Communications

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Systematic Review of Chemical Constituents in the Genus Lycium (Solanaceae)

(2017) Dan Qian et al.   MOLECULES

The Apostasia genome and the evolution of orchids

(2017) Guo-Qiang Zhang et al.   NATURE

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers

(2017) Chunling Chen et al.   PLoS One

Lack of S-RNase-Based Gametophytic Self-Incompatibility in Orchids Suggests That This System Evolved after the Monocot-Eudicot Split

(2017) Shan-Ce Niu et al.   Frontiers in Plant Science

The evolutionary history of plant T2/S-type ribonucleases

(2017) Karolis Ramanauskas et al.   PeerJ

Structure characterization, chemical and enzymatic degradation, and chain conformation of an acidic polysaccharide from Lycium barbarum L.

(2016) Wei Liu et al.   CARBOHYDRATE POLYMERS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Phylogenomics reveals surprising sets of essential and dispensable clades of MIKCc-group MADS-box genes in flowering plants

(2015) Lydia Gramzow et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

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

(2015) Christopher C Chang et al.   GigaScience

Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia

(2015) Ken-ichi Kubo et al.   Nature Plants

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Galactosyltransferases from Arabidopsis thaliana in the biosynthesis of type II arabinogalactan: molecular interaction enhances enzyme activity

(2014) Adiphol Dilokpimol et al.   BMC PLANT BIOLOGY

Comparative analysis of carotenoid accumulation in two goji (Lycium barbarum L. and L. ruthenicumMurr.) fruits

(2014) Yongliang Liu et al.   BMC PLANT BIOLOGY

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

(2014) Hideki Hirakawa et al.   DNA RESEARCH

Validated Method for the Analysis of Goji Berry, a Rich Source of Zeaxanthin Dipalmitate

(2014) Anastasia Karioti et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Transcriptional control of fleshy fruit development and ripening

(2014) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

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

(2014) Seungill Kim et al.   NATURE GENETICS

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Secondary Cell Walls: Biosynthesis, Patterned Deposition and Transcriptional Regulation

(2014) Ruiqin Zhong et al.   PLANT AND CELL PHYSIOLOGY

A Conserved Network of Transcriptional Activators and Repressors Regulates Anthocyanin Pigmentation in Eudicots

(2014) Nick W. Albert et al.   PLANT CELL

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

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

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

(2014) Nicolas Sierro et al.   Nature Communications

Fruit Development and Ripening

(2013) Graham B. Seymour et al.   Annual Review of Plant Biology

Evolving Views of Pectin Biosynthesis

(2013) Melani A. Atmodjo et al.   Annual Review of Plant Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Co-expression of cell-wall related genes: new tools and insights

(2012) Colin Ruprecht et al.   Frontiers in Plant Science

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity

(2011) G. R. Rodriguez et al.   PLANT PHYSIOLOGY

Molecular Analysis of a Family of Arabidopsis Genes Related to Galacturonosyltransferases

(2011) Y. Kong et al.   PLANT PHYSIOLOGY

Transcriptional networks for lignin biosynthesis: more complex than we thought?

(2011) Qiao Zhao et al.   TRENDS IN PLANT SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Functional gametophytic self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae)

(2010) J S Miller et al.   HEREDITY

Differential expression of candidate genes for lignin biosynthesis under drought stress in maize leaves

(2010) Y. Hu et al.   JOURNAL OF APPLIED GENETICS

Petunia nectar proteins have ribonuclease activity

(2010) Melissa S. Hillwig et al.   JOURNAL OF EXPERIMENTAL BOTANY

Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants

(2010) Jullyana Cristina Magalhães Silva Moura et al.   Journal of Integrative Plant Biology

Out of America to Africa or Asia: Inference of Dispersal Histories Using Nuclear and Plastid DNA and the S-RNase Self-incompatibility Locus

(2010) Jill S. Miller et al.   MOLECULAR BIOLOGY AND EVOLUTION

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

PEP1 regulates perennial flowering in Arabis alpina

(2009) Renhou Wang et al.   NATURE

An S-RNase-Based Gametophytic Self-Incompatibility System Evolved Only Once in Eudicots

(2008) Jorge Vieira et al.   JOURNAL OF MOLECULAR EVOLUTION

InterPro: the integrative protein signature database

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