Insights from the first genome assembly of Onion (Allium cepa)

Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.

(2021) Satoshi Fujito et al.   BMC GENOMICS

Building near-complete plant genomes

(2020) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Construction of an Onion (Allium cepa L.) Genetic Linkage Map Using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

(2020) Yousoo Choi et al.   Plants-Basel

A chromosome-level genome assembly of garlic (Allium sativum L.) provides insights into genome evolution and allicin biosynthesis

(2020) Xiudong Sun et al.   Molecular Plant

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

(2020) Marina Athanasouli et al.   BMC GENOMICS

A quick guide for student-driven community genome annotation

(2019) Prashant S. Hosmani et al.   PLoS Computational Biology

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order

(2019) Ludmila Khrustaleva et al.   Scientific Reports

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

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

(2017) Alex Harkess et al.   Nature Communications

RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum—A. cepa monosomic addition lines

(2017) Mostafa Abdelrahman et al.   PLoS One

SNP-markers in Allium species to facilitate introgression breeding in onion

(2016) Olga E. Scholten et al.   BMC PLANT BIOLOGY

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Construction of a draft reference transcripts of onion (Allium cepa) using long-read sequencing

(2016) Seong-Han Sohn et al.   Plant Biotechnology Reports

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

(2016) Obed Ramírez-Sánchez et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

(2016) Chengxi Ye et al.   Scientific Reports

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)

(2015) Rina Kamenetsky et al.   BMC GENOMICS

High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion

(2015) Ludmila Khrustaleva et al.   THEORETICAL AND APPLIED GENETICS

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium

(2015) Marcela Víquez-Zamora et al.   BMC GENOMICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

(2014) Juliana Stival Sena et al.   BMC PLANT BIOLOGY

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

(2014) S. Kim et al.   DNA RESEARCH

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes

(2013) C. Vitte et al.   ANNALS OF BOTANY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion

(2013) Christopher von Kohn et al.   GENOME

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

(2013) Jill L. Wegrzyn et al.   PLoS One

Transcriptome sequencing to produce SNP-based genetic maps of onion

(2013) J. Duangjit et al.   THEORETICAL AND APPLIED GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

AlliumMap-A comparative genomics resource for cultivated Allium vegetables

(2012) John McCallum et al.   BMC GENOMICS

Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations

(2012) Samantha Baldwin et al.   MOLECULAR BREEDING

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

Chromosomal Organization and Sequence Diversity of Genes Encoding Lachrymatory Factor Synthase in Allium cepa L.

(2012) Noriya Masamura et al.   G3-Genes Genomes Genetics

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Exploring giant plant genomes with next-generation sequencing technology

(2011) Laura J. Kelly et al.   CHROMOSOME RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration

(2008) Jernej Jakše et al.   MOLECULAR GENETICS AND GENOMICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH