Genome assembly, annotation, and comparative analysis of the cattail Typha latifolia

Genetic structure in hybrids and progenitors provides insight into processes underlying an invasive cattail (Typha × glauca) hybrid zone

(2020) Sara Pieper et al.   HEREDITY

Discovery and population genomics of structural variation in a songbird genus

(2020) Matthias H. Weissensteiner et al.   Nature Communications

Salinity, not genetic incompatibilities, limits the establishment of the invasive hybrid cattail Typha  ×  glauca in coastal wetlands

(2020) Kathryn Tisshaw et al.   Ecology and Evolution

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

(2019) Scott A. Taylor et al.   Nature Ecology & Evolution

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

(2019) Ling Xu et al.   NUCLEIC ACIDS RESEARCH

Typha (Cattail) Invasion in North American Wetlands: Biology, Regional Problems, Impacts, Ecosystem Services, and Management

(2019) Sheel Bansal et al.   WETLANDS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Understanding evolution in Poales: Insights from Eriocaulaceae plastome

(2019) Ashwini M. Darshetkar et al.   PLoS One

Characterization of the complete chloroplast genome sequence of wetland macrophyte Typha orientalis (Typhaceae)

(2019) Zhen-Dian Liu et al.   Mitochondrial DNA Part B-Resources

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

(2018) Edwin A. Solares et al.   G3-Genes Genomes Genetics

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Asymmetric Hybridization in Cattails (Typha spp.) and Its Implications for the Evolutionary Maintenance of Native Typha latifolia

(2017) Sara J. Pieper et al.   JOURNAL OF HEREDITY

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

The draft genome of MD-2 pineapple using hybrid error correction of long reads

(2016) Raimi M. Redwan et al.   DNA RESEARCH

Typha invasion associated with reduced aquatic macroinvertebrate abundance in northern Lake Huron coastal wetlands

(2016) Beth A. Lawrence et al.   JOURNAL OF GREAT LAKES RESEARCH

Hybridization in Plants: Old Ideas, New Techniques

(2016) Benjamin E. Goulet et al.   PLANT PHYSIOLOGY

The number of known plants species in the world and its annual increase

(2016) MAARTEN J.M. CHRISTENHUSZ et al.   Phytotaxa

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

(2016) Chengxi Ye et al.   Scientific Reports

Heterosis in invasive F1 cattail hybrids (Typha × glauca)

(2015) Lisa Zapfe et al.   AQUATIC BOTANY

Hybrid Typha×glauca outperforms native T. latifolia under contrasting water depths in a common garden

(2015) Adèle L. Bunbury-Blanchette et al.   BASIC AND APPLIED ECOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Comparison of genetic diversity in four Typha species (Poales, Typhaceae) from China

(2015) Beibei Zhou et al.   HYDROBIOLOGIA

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

(2015) Yi Wang et al.   NUCLEIC ACIDS RESEARCH

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Effects of invasive Typha × glauca on wetland nutrient pools, denitrification, and bacterial communities are influenced by time since invasion

(2014) Pamela Geddes et al.   AQUATIC ECOLOGY

Denitrification in a Laurentian Great Lakes coastal wetland invaded by hybrid cattail (Typha × glauca)

(2014) Shane C. Lishawa et al.   AQUATIC SCIENCES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

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

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

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

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

Regional differences in the abundance of native, introduced, and hybrid Typha spp. in northeastern North America influence wetland invasions

(2013) Joanna Freeland et al.   BIOLOGICAL INVASIONS

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

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

Nowhere to Invade: Rumex crispus and Typha latifolia Projected to Disappear under Future Climate Scenarios

(2013) Zhonglin Xu et al.   PLoS One

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Intercontinental dispersal of Typha angustifolia and T. latifolia between Europe and North America has implications for Typha invasions

(2012) Claudia Ciotir et al.   BIOLOGICAL INVASIONS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ruibang Luo et al.   GigaScience

Molecular genetic data reveal hybridization between Typha angustifolia and Typha latifolia across a broad spatial scale in eastern North America

(2011) Heather Kirk et al.   AQUATIC BOTANY

Mechanisms of dominance by the invasive hybrid cattail Typha × glauca

(2011) Daniel J. Larkin et al.   BIOLOGICAL INVASIONS

Species-specific SSR alleles for studies of hybrid cattails (Typha latifolia × T. angustifolia ; Typhaceae) in North America

(2010) Allison A. Snow et al.   AMERICAN JOURNAL OF BOTANY

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

(2010) Mary M. Guisinger et al.   JOURNAL OF MOLECULAR EVOLUTION

Litter drives ecosystem and plant community changes in cattail invasion

(2009) Emily C. Farrer et al.   ECOLOGICAL APPLICATIONS

Patterns of environmental change associated withTypha xglauca invasion in a Great Lakes coastal wetland

(2009) Nancy C. Tuchman et al.   WETLANDS

Plant community, primary productivity, and environmental conditions following wetland re-establishment in the Sacramento-San Joaquin Delta, California

(2009) Robin L. Miller et al.   WETLANDS ECOLOGY AND MANAGEMENT