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

Transcriptomic Analysis of Seed Germination Under Salt Stress in Two Desert Sister Species (Populus euphratica and P. pruinosa)

(2019) Caihua Zhang et al.   Frontiers in Genetics

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing

(2019) Ruby Dhar et al.   GigaScience

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection

(2019) Mingcheng Wang et al.   NEW PHYTOLOGIST

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae)

(2018) Ran Zhou et al.   MOLECULAR GENETICS AND GENOMICS

Ethylene Signaling Modulates Cortical Microtubule Reassembly in Response to Salt Stress

(2018) Liru Dou et al.   PLANT PHYSIOLOGY

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

(2018) Sergei A. Filichkin et al.   Frontiers in Plant Science

A small peptide modulates stomatal control via abscisic acid in long-distance signalling

(2018) Fuminori Takahashi et al.   NATURE

Genome sequence and genetic transformation of a widely distributed and cultivated poplar

(2018) Jianchao Ma et al.   PLANT BIOTECHNOLOGY JOURNAL

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Database Resources of the BIG Data Center in 2019

(2018) et al.   NUCLEIC ACIDS RESEARCH

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

(2018) Yao-Cheng Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-base-resolution methylomes of Populus euphratica reveal the association between DNA methylation and salt stress

(2018) Yutao Su et al.   Tree Genetics & Genomes

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Phospholipases Dζ1 and Dζ2 have distinct roles in growth and antioxidant systems in Arabidopsis thaliana responding to salt stress

(2017) Ahlem Ben Othman et al.   PLANTA

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

(2017) Tao Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New technologies boost genome quality

(2017) Elizabeth Pennisi   SCIENCE

Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings

(2017) Le Yu et al.   Genes

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral “Salicoid” Genome Duplication

(2016) Jing Hou et al.   Genome Biology and Evolution

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Light affects salt stress-induced transcriptional memory ofP5CS1inArabidopsis

(2016) Xuan Jun Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct patterns of natural selection in Na+/H+antiporter genes inPopulus euphraticaandPopulus pruinosa

(2016) Yuxia Wu et al.   Ecology and Evolution

Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica

(2016) Hui Duan et al.   Frontiers in Plant Science

Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars

(2016) Jianchao Ma et al.   Genes

Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation

(2016) Xiaodong Ma et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

NaCl-elicited, vacuolar Ca2+ release facilitates prolonged cytosolic Ca2+ signaling in the salt response of Populus euphratica cells

(2015) Xuan Zhang et al.   CELL CALCIUM

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

(2014) Jinhuan Chen et al.   BMC GENOMICS

The willow genome and divergent evolution from poplar after the common genome duplication

(2014) Xiaogang Dai et al.   CELL RESEARCH

On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats

(2014) ANDREA POLLE et al.   PLANT CELL AND ENVIRONMENT

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

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

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Genomic insights into salt adaptation in a desert poplar

(2013) Tao Ma et al.   Nature Communications

Overexpression of Arabidopsis translationally controlled tumor protein gene AtTCTP enhances drought tolerance with rapid ABA-induced stomatal closure

(2012) Yong-Min Kim et al.   MOLECULES AND CELLS

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

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

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Genome-scale transcriptome analysis of the desert poplar, Populus euphratica

(2011) Q. Qiu et al.   TREE PHYSIOLOGY

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

(2009) Marieke Louwers et al.   Nature Protocols

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY