Phylogenomic classification and synteny network analyses deciphered the evolutionary landscape of aldo–keto reductase (AKR) gene superfamily in the plant kingdom

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Analysis of Aldo–Keto Reductase Gene Family and Their Responses to Salt, Drought, and Abscisic Acid Stresses in Medicago truncatula

(2020) Jie Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage‐specific patterns

(2020) Merijn H.L. Kerstens et al.   PLANT JOURNAL

Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants

(2020) Bei Gao et al.   Plant Methods

Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa

(2020) Weike Duan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin

(2020) Alejandro Pereira-Santana et al.   PLoS Computational Biology

A concise appraisal of lipid oxidation and lipoxidation in higher plants

(2019) Juan de Dios Alché   Redox Biology

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

(2019) Tao Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Aldo-keto reductase metabolizes glyphosate and confers glyphosate resistance in Echinochloa colona

(2019) Lang Pan et al.   PLANT PHYSIOLOGY

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions in l-tartaric acid biosynthesis from vitamin C in Vitis vinifera

(2019) Yong Jia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dissecting the Genome-Wide Evolution and Function of R2R3-MYB Transcription Factor Family in Rosa chinensis

(2019) Yu Han et al.   Genes

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Involvement of chalcone reductase (CHR) in the soybean isoflavone metabolon: Identification of GmCHR5 that interacts with 2-hydroxyisoflavanone synthase

(2018) Ryo Mameda et al.   PLANT JOURNAL

Reactive oxygen species in plant development

(2018) Amna Mhamdi et al.   DEVELOPMENT

Dissecting the genomic diversification of LATE EMBRYOGENESIS ABUNDANT (LEA) protein gene families in plants

(2018) Mariana Aline Silva Artur et al.   Genome Biology and Evolution

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

(2018) Yi Zheng et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

(2017) Tao Zhao et al.   PLANT CELL

ROS Are Good

(2017) Ron Mittler   TRENDS IN PLANT SCIENCE

IPC – Isoelectric Point Calculator

(2016) Lukasz P. Kozlowski   Biology Direct

Reactive oxygen species, abiotic stress and stress combination

(2016) Feroza K. Choudhury et al.   PLANT JOURNAL

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

The aldo-keto reductases (AKRs): Overview

(2015) Trevor M. Penning   CHEMICO-BIOLOGICAL INTERACTIONS

Plant aldo-keto reductases (AKRs) as multi-tasking soldiers involved in diverse plant metabolic processes and stress defense: A structure-function update

(2015) Debashree Sengupta et al.   JOURNAL OF PLANT PHYSIOLOGY

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Lipid Peroxide-Derived Short-Chain Carbonyls Mediate Hydrogen Peroxide-Induced and Salt-Induced Programmed Cell Death in Plants

(2015) Md. Sanaullah Biswas et al.   PLANT PHYSIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Characterization of an uncharacterized aldo-keto reductase gene from peach and its role in abiotic stress tolerance

(2014) Yoshinori Kanayama et al.   PHYTOCHEMISTRY

ROS-Mediated Lipid Peroxidation and RES-Activated Signaling

(2013) Edward E. Farmer et al.   Annual Review of Plant Biology

Redox Signaling in Plants

(2013) Christine H. Foyer et al.   ANTIOXIDANTS & REDOX SIGNALING

ROS as key players in plant stress signalling

(2013) A. Baxter et al.   JOURNAL OF EXPERIMENTAL BOTANY

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Banana Genome Hub

(2013) Gaëtan Droc et al.   Database-The Journal of Biological Databases and Curation

Crystal Structure of Perakine Reductase, Founding Member of a Novel Aldo-Keto Reductase (AKR) Subfamily That Undergoes Unique Conformational Changes during NADPH Binding

(2012) Lianli Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Reactive carbonyl species: Their production from lipid peroxides, action in environmental stress, and the detoxification mechanism

(2012) Jun’ichi Mano   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Plant tropane alkaloid biosynthesis evolved independently in the Solanaceae and Erythroxylaceae

(2012) J. Jirschitzka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of a pyridoxal reductase involved in the vitamin B6 salvage pathway in Arabidopsis

(2011) Sonia Herrero et al.   PLANT MOLECULAR BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

(2010) Sarvajeet Singh Gill et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genome-Wide Comparative Gene Family Classification

(2010) Christian Frech et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Characterization of Two Novel Aldo–Keto Reductases from Arabidopsis: Expression Patterns, Broad Substrate Specificity, and an Open Active-Site Structure Suggest a Role in Toxicant Metabolism Following Stress

(2009) Paul J. Simpson et al.   JOURNAL OF MOLECULAR BIOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

ROS in biotic interactions

(2009) Miguel Angel Torres   PHYSIOLOGIA PLANTARUM

ROS generation in plants: Boon or bane?

(2009) N. Garg et al.   PLANT BIOSYSTEMS