Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity

The complete chloroplast genome of Ficus pumila, a functional plant in East Asia

(2022) DanYang Liang et al.   Mitochondrial DNA Part B-Resources

Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species

(2022) Yuying Huang et al.   BMC PLANT BIOLOGY

The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms

(2021) Shubham K. Jaiswal et al.   iScience

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

(2021) Gang Wang et al.   Nature Communications

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

Genome sequencing of turmeric provides evolutionary insights into its medicinal properties

(2021) Abhisek Chakraborty et al.   Communications Biology

The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig ( F. carica )

(2020) Kenta Shirasawa et al.   PLANT JOURNAL

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera)

(2020) Hanno Schmidt et al.   G3-Genes Genomes Genetics

Signaling Role of Glutamate in Plants

(2020) Xue-Mei Qiu et al.   Frontiers in Plant Science

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Arabidopsis AtMPV17, a homolog of mice MPV17, enhances osmotic stress tolerance

(2020) Jiwoong Wi et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution

(2020) Xingtan Zhang et al.   CELL

On tree longevity

(2020) Gianluca Piovesan et al.   NEW PHYTOLOGIST

Defence mechanisms of Ficus: pyramiding strategies to cope with pests and pathogens

(2019) Cloé Villard et al.   PLANTA

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

The Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Is Critical for Abiotic Stress Response in Wheat

(2019) Xixi Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

(2019) Liyi Zhang et al.   Nature Communications

1-Aminocyclopropane-1-Carboxylic Acid Oxidase (ACO): The Enzyme That Makes the Plant Hormone Ethylene

(2019) Maarten Houben et al.   Frontiers in Plant Science

Arabidopsis thionin-like genes are involved in resistance against the beet-cyst nematode (Heterodera schachtii)

(2019) Bachar Almaghrabi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome

(2019) Quanxin Bi et al.   GigaScience

Systematic Analysis and Functional Validation of Citrus XTH Genes Reveal the Role of Csxth04 in Citrus Bacterial Canker Resistance and Tolerance

(2019) Qiang Li et al.   Frontiers in Plant Science

The Plant DNA C‐values database (release 7.1): an updated online repository of plant genome size data for comparative studies

(2019) Jaume Pellicer et al.   NEW PHYTOLOGIST

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Epigenetic patterns within the haplotype phased fig ( Ficus carica L.) genome

(2019) Gabriele Usai et al.   PLANT JOURNAL

Comparative analysis of corrected tiger genome provides clues to its neuronal evolution

(2019) Parul Mittal et al.   Scientific Reports

Manipulation and Sensing of Auxin Metabolism, Transport and Signaling

(2018) Kosuke Fukui et al.   PLANT AND CELL PHYSIOLOGY

STRESS INDUCED FACTOR 2, a Leucine-Rich Repeat Kinase Regulates Basal Plant Pathogen Defense

(2018) Ning Yuan et al.   PLANT PHYSIOLOGY

Comparative multi-omics analysis reveals diverse latex-based defense strategies against pests among latex-producing organs of the fig tree (Ficus carica)

(2018) Sakihito Kitajima et al.   PLANTA

The genus Ficus (Moraceae) used in diet: Its plant diversity, distribution, traditional uses and ethnopharmacological importance

(2018) Yinxian Shi et al.   JOURNAL OF ETHNOPHARMACOLOGY

Limits to Tree Growth and Longevity

(2018) Sergi Munné-Bosch   TRENDS IN PLANT SCIENCE

ACR11 modulates levels of reactive oxygen species and salicylic acid-associated defense response in Arabidopsis

(2018) Shashi Kant Singh et al.   Scientific Reports

In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins

(2018) Ankita Sharma et al.   Frontiers in Microbiology

Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird

(2018) Shubham K. Jaiswal et al.   Frontiers in Genetics

Tigmint: correcting assembly errors using linked reads from large molecules

(2018) Shaun D. Jackman et al.   BMC BIOINFORMATICS

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arabidopsis WRKY45 Interacts with the DELLA Protein RGL1 to Positively Regulate Age-Triggered Leaf Senescence

(2017) Ligang Chen et al.   Molecular Plant

Docking-based screening of Ficus religiosa phytochemicals as inhibitors of human histamine H2 receptor

(2017) Ashutosh Mani et al.   Pharmacognosy Magazine

Gain-of-Function Mutants of the Cytokinin Receptors AHK2 and AHK3 Regulate Plant Organ Size, Flowering Time and Plant Longevity

(2017) Isabel Bartrina et al.   PLANT PHYSIOLOGY

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

(2017) Kazuki Mori et al.   Scientific Reports

KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences

(2017) Dominik R. Laetsch et al.   G3-Genes Genomes Genetics

The Importance ofFicus(Moraceae) Trees for Tropical Forest Restoration

(2016) H. Eden W. Cottee-Jones et al.   BIOTROPICA

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

AGOUTI: improving genome assembly and annotation using transcriptome data

(2016) Simo V. Zhang et al.   GigaScience

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A role for the mevalonate pathway in early plant symbiotic signaling

(2015) Muthusubramanian Venkateshwaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

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

Tree immunity: growing old without antibodies

(2014) Peri A. Tobias et al.   TRENDS IN PLANT SCIENCE

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The Role of Hormones in the Aging of Plants - A Mini-Review

(2013) Mamoona Khan et al.   GERONTOLOGY

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

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

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

Auxin: a master regulator in plant root development

(2013) Shivani Saini et al.   PLANT CELL REPORTS

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

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Traditional uses, phytochemistry and pharmacology of Ficus religiosa: A review

(2011) Damanpreet Singh et al.   JOURNAL OF ETHNOPHARMACOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

RPK2 is an essential receptor-like kinase that transmits the CLV3 signal in Arabidopsis

(2010) A. Kinoshita et al.   DEVELOPMENT

Arabidopsis Basic Leucine-Zipper Transcription Factors TGA9 and TGA10 Interact with Floral Glutaredoxins ROXY1 and ROXY2 and Are Redundantly Required for Anther Development

(2010) J. Murmu et al.   PLANT PHYSIOLOGY

The Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Is Critical for Viable Pollen Development in Arabidopsis

(2010) J. Munoz-Bertomeu et al.   PLANT PHYSIOLOGY

Ability of crassulacean acid metabolism plants to overcome interacting stresses in tropical environments

(2010) Ulrich Lüttge   AoB Plants

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The reproductive success of Ficus altissima and its pollinator in a strongly seasonal environment: Xishuangbanna, Southwestern China

(2009) Yan-Qiong Peng et al.   PLANT ECOLOGY

Effect of Pollination on Floral Longevity and Costs of Delaying Fertilization in the Out-crossing Polygala vayredae Costa (Polygalaceae)

(2008) Sílvia Castro et al.   ANNALS OF BOTANY