4.7 Article

Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Plant Sciences

Heterologous Expression of Camellia sinensis Late Embryogenesis Abundant Protein Gene 1 (CsLEA1) Confers Cold Stress Tolerance in Escherichia coli and Yeast

Tong Gao et al.

Summary: The CsLEA1 protein, identified in a tea plant, plays a crucial role in enhancing cold stress tolerance by regulating gene expression and promoting hydrophilicity. This suggests its potential application in molecular breeding for improving stress resilience in tea plants.

HORTICULTURAL PLANT JOURNAL (2021)

Article Biotechnology & Applied Microbiology

De novo assembly of a wild pear (Pyrus betuleafolia) genome

Xingguang Dong et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

Article Biochemistry & Molecular Biology

Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica)

Zhiyang Zhang et al.

MOLECULAR ECOLOGY RESOURCES (2020)

Article Biochemistry & Molecular Biology

Long-read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

Tao Zhang et al.

MOLECULAR ECOLOGY RESOURCES (2020)

Letter Biotechnology & Applied Microbiology

A high-quality walnut genome assembly reveals extensive gene expression divergences after whole-genome duplication

Junpei Zhang et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

Article Plant Sciences

Comparative genomics of six Juglans species reveals disease-associated gene family contractions

Alexander J. Trouern-Trend et al.

PLANT JOURNAL (2020)

Article Biochemistry & Molecular Biology

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

Chengjie Chen et al.

MOLECULAR PLANT (2020)

Article Biotechnology & Applied Microbiology

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Jae Young Choi et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

Bo-Wen Zhang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

The Pfam protein families database in 2019

Sara El-Gebali et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Matthew Z. DeMaere et al.

GENOME BIOLOGY (2019)

Article Genetics & Heredity

Genomic Variation Among and Within Six Juglans Species

Kristian A. Stevens et al.

G3-GENES GENOMES GENETICS (2018)

Article Biochemical Research Methods

MUMmer4: A fast and versatile genome alignment system

Guillaume Marcais et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Plant Sciences

The Phytogeographic History of Common Walnut in China

Xiaojia Feng et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Biochemistry & Molecular Biology

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

Aron Marchler-Bauer et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

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

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Biochemical Research Methods

Assemblytics: a web analytics tool for the detection of variants from an assembly

Maria Nattestad et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Horticulture

Natural Hybridization between Persian Walnut and Chinese Walnut Revealed by Simple Sequence Repeat Markers

Zhan Shu et al.

JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

GSDS 2.0: an upgraded gene feature visualization server

Bo Hu et al.

BIOINFORMATICS (2015)

Article Chemistry, Applied

A new naphthalenone isolated from the green walnut husks of Juglans mandshurica Maxim.

Guang Chen et al.

NATURAL PRODUCT RESEARCH (2015)

Article Biotechnology & Applied Microbiology

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nicolas Servant et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Pharmacology & Pharmacy

Application of ggplot2 to Pharmacometric Graphics

K. Ito et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2013)

Article Chemistry, Medicinal

Three New Naphthalenyl Glycosides from the Root Bark of Juglans cathayensis

Jia-Xiang Sun et al.

CHEMICAL & PHARMACEUTICAL BULLETIN (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

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

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Biochemical Research Methods

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Carson Holt et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Plant Sciences

Naphthoquinones from the root barks of Juglans cathayensis Dode

Heng-Yi Yu et al.

JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH (2011)

Article Genetics & Heredity

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Dapeng Wang et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2010)

Article Biochemical Research Methods

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

Andrew D. Johnson et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

Sudhir Kumar et al.

BRIEFINGS IN BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

The Pfam protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Forestry

Molecular phylogeny of Juglans (Juglandaceae):: a biogeographic perspective

Mallikarjuna K. Aradhya et al.

TREE GENETICS & GENOMES (2007)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Zhao Xu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

CAFE: a computational tool for the study of gene family evolution

T De Bie et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

PILER: identification and classification of genomic repeats

RC Edgar et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

TD Wu et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Automated generation of heuristics for biological sequence comparison

GS Slater et al.

BMC BIOINFORMATICS (2005)

Review Biotechnology & Applied Microbiology

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

EV Koonin et al.

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

B Boeckmann et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemical Research Methods

InterProScan - an integration platform for the signature-recognition methods in InterPro

EM Zdobnov et al.

BIOINFORMATICS (2001)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemistry & Molecular Biology

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

A Bairoch et al.

NUCLEIC ACIDS RESEARCH (2000)