A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

(2020) Minghui Kang et al.   Horticulture Research

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

(2020) Gai Huang et al.   NATURE GENETICS

Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa

(2020) Haitao Chen et al.   Nature Communications

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

(2020) Shu-Fen Li et al.   Horticulture Research

Cellulose Synthesis – Central Components and Their Evolutionary Relationships

(2019) Edwin R. Lampugnani et al.   TRENDS IN PLANT SCIENCE

Author Correction: Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Lignin biosynthesis and its integration into metabolism

(2019) Ruben Vanholme et al.   CURRENT OPINION IN BIOTECHNOLOGY

A reference genome for pea provides insight into legume genome evolution

(2019) Jonathan Kreplak et al.   NATURE GENETICS

MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses

(2019) Qiang Zhou et al.   PeerJ

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms

(2019) Shengdan Wu et al.   Molecular Plant

A high-quality Actinidia chinensis (kiwifruit) genome

(2019) Haolin Wu et al.   Horticulture Research

Agronomic Performance and Lignin Content of HCT Down-Regulated Alfalfa (Medicago sativa L.)

(2018) Kishor Bhattarai et al.   BioEnergy Research

Physiological and Proteomic Responses of Contrasting Alfalfa (Medicago sativa L.) Varieties to PEG-Induced Osmotic Stress

(2018) Cuimei Zhang et al.   Frontiers in Plant Science

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

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

Development and commercialization of reduced lignin alfalfa

(2018) Jaime Barros et al.   CURRENT OPINION IN BIOTECHNOLOGY

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform

(2017) Jinpeng Wang et al.   PLANT PHYSIOLOGY

On the study of microbial transcriptomes using second- and third-generation sequencing technologies

(2016) Sang Chul Choi   JOURNAL OF MICROBIOLOGY

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Antioxidant effects of alfalfa can improve iron oxide nanoparticle damage: Invivo and invitro studies

(2016) Leila Sadeghi et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

(2015) George P. Tiley et al.   BMC EVOLUTIONARY BIOLOGY

Identification and distribution of the NBS-LRR gene family in the Cassava genome

(2015) Roberto Lozano et al.   BMC GENOMICS

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

Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches

(2015) Hsin-Hung Lin et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Specificity control for read alignments using an artificial reference genome-guided false discovery rate

(2013) Sven H. Giese et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa

(2013) Zhipeng Liu et al.   PLoS One

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

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Applied Genetics and Genomics in Alfalfa Breeding

(2012) Xuehui Li et al.   Agronomy-Basel

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Phytochemical and pharmacological potential ofMedicago sativa: A review

(2010) Kundan Singh Bora et al.   PHARMACEUTICAL BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Cheap third-generation sequencing

(2009) Nicole Rusk   NATURE METHODS

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY