The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).

PubWeight™: 0.75‹?›

🔗 View Article (PMID 28431014)

Published in DNA Res on April 01, 2017

Authors

Yongbin Zhuang1,2, Erin A Tripp1,2

Author Affiliations

1: Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA.
2: Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA.

Articles cited by this

(truncated to the top 100)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81

Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol (2012) 62.36

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res (2002) 47.62

PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68

Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68

ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20

BLAST+: architecture and applications. BMC Bioinformatics (2009) 36.53

Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42

Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41

Scaffolding pre-assembled contigs using SSPACE. Bioinformatics (2010) 23.27

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res (2003) 18.69

UniProt: a hub for protein information. Nucleic Acids Res (2014) 16.72

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res (2010) 10.53

The tomato genome sequence provides insights into fleshy fruit evolution. Nature (2012) 9.47

An improved general amino acid replacement matrix. Mol Biol Evol (2008) 9.36

Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics (2003) 8.92

Gene finding in novel genomes. BMC Bioinformatics (2004) 8.64

Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 7.44

UniProtKB/Swiss-Prot. Methods Mol Biol (2007) 7.05

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics (2015) 5.24

The MaSuRCA genome assembler. Bioinformatics (2013) 5.07

MYB transcription factors in Arabidopsis. Trends Plant Sci (2010) 4.64

Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature (2003) 4.17

Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics (2011) 4.15

Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci U S A (2007) 4.13

The evolutionary consequences of polyploidy. Cell (2007) 3.80

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40

Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color. Plant Cell (1999) 3.10

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Maize anthocyanin regulatory gene pl is a duplicate of c1 that functions in the plant. Plant Cell (1993) 2.77

Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J (1998) 2.71

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res (2012) 2.68

PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res (2007) 2.61

PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell (2009) 2.43

The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant J (2007) 2.28

A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr Biol (2005) 2.25

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet (2014) 2.19

Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci U S A (1994) 2.06

The draft genome and transcriptome of Cannabis sativa. Genome Biol (2011) 2.03

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A (2014) 1.91

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact (2012) 1.84

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife (2013) 1.84

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol (2008) 1.68

HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. New Phytol (2007) 1.58

Architecture and evolution of a minute plant genome. Nature (2013) 1.57

Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol (2007) 1.50

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol (2013) 1.48

Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J (2008) 1.46

Flavanols and anthocyanins in cardiovascular health: a review of current evidence. Int J Mol Sci (2010) 1.43

Members of an R2R3-MYB transcription factor family in Petunia are developmentally and environmentally regulated to control complex floral and vegetative pigmentation patterning. Plant J (2011) 1.42

Alteration of a single amino acid changes the substrate specificity of dihydroflavonol 4-reductase. Plant J (2001) 1.41

Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput Biol (2014) 1.36

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics (2012) 1.36

Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics (2013) 1.35

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics (2014) 1.32

MYB72 is required in early signaling steps of rhizobacteria-induced systemic resistance in Arabidopsis. Plant Physiol (2008) 1.31

Is floral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae). Evolution (2008) 1.30

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proc Natl Acad Sci U S A (2013) 1.21

MYB transcription factor genes as regulators for plant responses: an overview. Physiol Mol Biol Plants (2013) 1.15

Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics (2006) 1.10

Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol (2013) 1.10

Flower color microevolution in wild radish: evolutionary response to pollinator-mediated selection. Am Nat (2004) 1.09

The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution. PLoS One (2013) 1.08

A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci (2013) 1.06

GMATo: A novel tool for the identification and analysis of microsatellites in large genomes. Bioinformation (2013) 1.04

Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res (2014) 1.04

De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Plant Physiol (2014) 1.02

MYB72, a node of convergence in induced systemic resistance triggered by a fungal and a bacterial beneficial microbe. Plant Biol (Stuttg) (2009) 1.02

Why assembling plant genome sequences is so challenging. Biology (Basel) (2012) 1.02

Expansion and subfunctionalisation of flavonoid 3',5'-hydroxylases in the grapevine lineage. BMC Genomics (2010) 1.02

Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteomics Bioinformatics (2014) 0.97

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants (2016) 0.94

A chemical complementation approach reveals genes and interactions of flavonoids with other pathways. Plant J (2013) 0.94

Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol (2014) 0.94

The draft genome of Primula veris yields insights into the molecular basis of heterostyly. Genome Biol (2015) 0.94

Functional evolution of an anthocyanin pathway enzyme during a flower color transition. Mol Biol Evol (2012) 0.89

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics. Evol Bioinform Online (2010) 0.88

Characterization of Arabidopsis MYB transcription factor gene AtMYB17 and its possible regulation by LEAFY and AGL15. J Genet Genomics (2009) 0.88

Auxin homeostasis during lateral root development under drought condition. Plant Signal Behav (2009) 0.86

AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. New Phytol (2014) 0.84

Ecological transition predictably associated with gene degeneration. Mol Biol Evol (2014) 0.83

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep (2016) 0.83

Dihydroflavonol 4-reductase genes encode enzymes with contrasting substrate specificity and show divergent gene expression profiles in Fragaria species. PLoS One (2014) 0.82

Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species. Gene (2014) 0.82

AtMYB14 Regulates Cold Tolerance in Arabidopsis. Plant Mol Biol Report (2013) 0.81

Erratum to: A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 0.79

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol (2015) 0.79

Articles by these authors

The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). DNA Res (2017) 0.75