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

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

(2019) Shu-Fen Li et al.   Mobile DNA

Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA

(2019) Sergio S. Samoluk et al.   PLANTA

Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora

(2019) Jasmina Uzunović et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species

(2019) Deling Sun et al.   Horticulture Research

Characterization of the complete chloroplast genome of Asparagus setaceus

(2019) Jia-Rong Li et al.   Mitochondrial DNA Part B-Resources

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

(2018) Lauren Coombe et al.   BMC BIOINFORMATICS

Anthocyanins Accumulation and Molecular Analysis of Correlated Genes by Metabolome and Transcriptome in Green and Purple Asparaguses ( Asparagus Officinalis , L.)

(2018) Tingting Dong et al.   FOOD CHEMISTRY

Draft genome sequence ofCamellia sinensisvar.sinensisprovides insights into the evolution of the tea genome and tea quality

(2018) Chaoling Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

(2018) Jose Die et al.   Genes

The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans

(2018) Xiulian Yang et al.   Horticulture Research

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

(2017) Sergey Koren et al.   GENOME RESEARCH

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

(2017) Alex Harkess et al.   Nature Communications

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

(2017) Shu-Fen Li et al.   Genes

MYB transcription factor gene involved in sex determination inAsparagus officinalis

(2016) Kohji Murase et al.   GENES TO CELLS

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

(2015) Maria F. Norup et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

(2015) Alex Harkess et al.   NEW PHYTOLOGIST

The draft genome of Primula veris yields insights into the molecular basis of heterostyly

(2015) Michael D Nowak et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

(2015) René L. Warren et al.   GigaScience

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Analysis of Transposable Elements in the Genome of Asparagus officinalis from High Coverage Sequence Data

(2014) Shu-Fen Li et al.   PLoS One

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

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

Infernal 1.1: 100-fold faster RNA homology searches

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

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

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

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sex Chromosomes in Land Plants

(2011) Ray Ming et al.   Annual Review of Plant Biology

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Molecular phylogeny of the genus Asparagus (Asparagaceae) explains interspecific crossability between the garden asparagus (A. officinalis) and other Asparagus species

(2011) Shosei Kubota et al.   THEORETICAL AND APPLIED GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ethnoveterinary use of southern African plants and scientific evaluation of their medicinal properties

(2008) L.J. McGaw et al.   JOURNAL OF ETHNOPHARMACOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY