A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Diesel, Jose; Molano, Gary; Montecinos, Gabriel J.; DeWeese, Kelly; Calhoun, Sara; Kuo, Alan; Lipzen, Anna; Salamov, Asaf; Grigoriev, Igor V.; Reed, Daniel C.; Miller, Robert J.; Nuzhdin, Sergey V.; Alberto, Filipe

doi:10.1186/s12864-023-09658-x

Title: A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Abstract

Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploidmore »« less

Authors:: Diesel, Jose; Molano, Gary; Montecinos, Gabriel J.; DeWeese, Kelly; Calhoun, Sara; Kuo, Alan; Lipzen, Anna; Salamov, Asaf; Grigoriev, Igor V.; Reed, Daniel C.; Miller, Robert J.; Nuzhdin, Sergey V.; Alberto, Filipe

Publication Date:: Wed Sep 13 00:00:00 EDT 2023

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

OSTI Identifier:: 1999966

Alternate Identifier(s):: OSTI ID: 2283391

Grant/Contract Number:: FOA-0001726-1513; AC02-05CH11231

Resource Type:: Published Article

Journal Name:: BMC Genomics

Additional Journal Information:: Journal Name: BMC Genomics Journal Volume: 24 Journal Issue: 1; Journal ID: ISSN 1471-2164

Publisher:: Springer Science + Business Media

Country of Publication:: United Kingdom

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; Genome; Giant kelp; Macrocystis pyrifera; Brown macroalga; Population genetics

Citation Formats


                    Diesel, Jose, Molano, Gary, Montecinos, Gabriel J., DeWeese, Kelly, Calhoun, Sara, Kuo, Alan, Lipzen, Anna, Salamov, Asaf, Grigoriev, Igor V., Reed, Daniel C., Miller, Robert J., Nuzhdin, Sergey V., and Alberto, Filipe. A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera).  United Kingdom: N. p., 2023. 
Web.  doi:10.1186/s12864-023-09658-x.

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                    Diesel, Jose, Molano, Gary, Montecinos, Gabriel J., DeWeese, Kelly, Calhoun, Sara, Kuo, Alan, Lipzen, Anna, Salamov, Asaf, Grigoriev, Igor V., Reed, Daniel C., Miller, Robert J., Nuzhdin, Sergey V., & Alberto, Filipe. A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera).  United Kingdom.  https://doi.org/10.1186/s12864-023-09658-x

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                    Diesel, Jose, Molano, Gary, Montecinos, Gabriel J., DeWeese, Kelly, Calhoun, Sara, Kuo, Alan, Lipzen, Anna, Salamov, Asaf, Grigoriev, Igor V., Reed, Daniel C., Miller, Robert J., Nuzhdin, Sergey V., and Alberto, Filipe. Wed .  
"A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)".  United Kingdom.  https://doi.org/10.1186/s12864-023-09658-x.

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@article{osti_1999966,

  title        = {A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)},

  author       = {Diesel, Jose and Molano, Gary and Montecinos, Gabriel J. and DeWeese, Kelly and Calhoun, Sara and Kuo, Alan and Lipzen, Anna and Salamov, Asaf and Grigoriev, Igor V. and Reed, Daniel C. and Miller, Robert J. and Nuzhdin, Sergey V. and Alberto, Filipe},

  abstractNote = {Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.},

  doi          = {10.1186/s12864-023-09658-x},

  journal      = {BMC Genomics},

  number       = 1,

  volume       = 24,

  place        = {United Kingdom},

  year         = {Wed Sep 13 00:00:00 EDT 2023},

  month        = {Wed Sep 13 00:00:00 EDT 2023}

}

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Jurka, J.; Kapitonov, V. V.; Pavlicek, A.
Cytogenetic and Genome Research, Vol. 110, Issue 1-4
DOI: 10.1159/000084979

Global Ecology of the Giant Kelp Macrocystis
book, June 2007

Buschmann, Alejandro; Graham, Michael; Vasquez, Julio
Oceanography and Marine Biology
DOI: 10.1201/9781420050943.ch2

Fast two-stage phasing of large-scale sequence data
journal, October 2021

Browning, Brian L.; Tian, Xiaowen; Zhou, Ying
The American Journal of Human Genetics, Vol. 108, Issue 10
DOI: 10.1016/j.ajhg.2021.08.005

Similar Records in DOE PAGES and OSTI.GOV collections:

Sporophyte Stage Genes Exhibit Stronger Selection Than Gametophyte Stage Genes in Haplodiplontic Giant Kelp

Journal Article Molano, Gary ; Diesel, Jose ; Montecinos, Gabriel J. ; ... - Frontiers in Marine Science

Macrocystis pyrifera (giant kelp), a haplodiplontic brown macroalga that alternates between a macroscopic diploid (sporophyte) and a microscopic haploid (gametophyte) phase, provides an ideal system to investigate how ploidy background affects the evolutionary history of a gene. In M. pyrifera , the same genome is subjected to different selective pressures and environments as it alternates between haploid and diploid life stages. We assembled M. pyrifera gene models using available expression data and validated 8,292 genes models using the model alga Ectocarpus siliculosus . Differential expression analysis identified gene models expressed in either or both the haploid and diploid life stagesmore »« less
https://doi.org/10.3389/fmars.2021.774076
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera , across depth and season

Journal Article Konotchick, Talina ; Dupont, Christopher L. ; Valas, Ruben E. ; ... - New Phytologist

To increase knowledge of transcript diversity for the giant kelp, Macrocystis pyrifera, and assess gene expression across naturally occurring depth gradients in light, temperature and nutrients, we sequenced four cDNA libraries created from blades collected at the sea surface and at 18 m depth during the winter and summer. Comparative genomics cluster analyses revealed novel gene families (clusters) in existing brown alga expressed sequence tag data compared with other related algal groups, a pattern also seen with the addition of M. pyrifera sequences. Assembly of 228 Mbp of sequence generated c. 9000 isotigs and c. 12 000 open reading frames.more »« less
https://doi.org/10.1111/nph.12160

Full Text Available
Giant kelp genetic monitoring before and after disturbance reveals stable genetic diversity in Southern California

Journal Article Klingbeil, III, William H. ; Montecinos, G. J. ; Alberto, Filipe - Frontiers in Marine Science

Given the impacts of climate change and other anthropogenic stressors on marine systems, there is a need to accurately predict how species respond to changing environments and disturbance regimes. The use of genetic tools to monitor temporal trends in populations gives ecologists the ability to estimate changes in genetic diversity and effective population size that may be undetectable by traditional census methods. Although multiple studies have used temporal genetic analysis, they usually involve commercially important species, and rarely sample before and after disturbance. In this study, we run a temporal analysis of giant kelp, Macrocystis pyrifera , genetic diversity overmore »« less
https://doi.org/10.3389/fmars.2022.947393
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Seasonal or chronic nutrient limitations in the photic zone limit large-scale cultivation of seaweed (macroalgae) in much of the world's oceans, hindering the development of macroalgae as a biofuel feedstock. One possible solution is to supply nutrients using a diel depth-cycling approach, physically moving the macroalgae between deep nutrient-rich water at night and shallow depths within the photic zone during the day. This study tested the effects of depth-cycling on the growth, morphology, and chemical composition of the giant kelp Macrocystis pyrifera, a target species for renewable biomass production. Giant kelp grown under depth-cycling conditions had an average growth ratemore »« less
https://doi.org/10.1016/j.rser.2021.110747
Comparative effects of oil dispersants to the early life stages of topsmelt (Atherinops affinis) and kelp (Macrocystis pyrifera)

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The acute effects of two oilspill dispersants were compared using the early life stages of two common nearshore marine organisms: the topsmelt (Atherinops affinis), a common fish in bays and estuaries, and the giant kelp (Macrocystis pyrifera), a canopy-forming brown alga. Testing was done under closed, flow-through conditions, with spiked dispersant concentrations measured in real time using UV spectrophotometry. Both dispersants were composed of complex mixtures of anionic and non-ionic surfactants and solvents. Median-effect concentration data showed Atherinops tests to be more sensitive to both dispersants than Macrocystis tests, with values ranging from 48.2 to 72.9 ppm (LC50) and 73.0more »« less
https://doi.org/10.1897/1552-8618(1994)13[649:CEOODT]2.0.CO;2

Similar Records

Title: A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Abstract

Citation Formats

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites journal, January 1997

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1. journal, November 2015

Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera) journal, June 2020

QUAST: quality assessment tool for genome assemblies journal, February 2013

Nuclear DNA level and life cycle of kelps: Evidence for sex-specific polyteny in Macrocystis (Laminariales, Phaeophyceae) journal, January 2016

Unexpected cross-species contamination in genome sequencing projects journal, January 2014

A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida journal, January 2021

Seaweed breeding programs and progress in eastern Asian countries journal, September 2019

Breeding, economic traits evaluation, and commercial cultivation of a new Saccharina variety “Huangguan No. 1” journal, April 2014

The Effects of Variable Settlement and Early Competition on Patterns of Kelp Recruitment journal, April 1990

Scaling up bioethanol production from the farmed brown macroalga Macrocystis pyrifera in Chile: Kelp based bioethanol production journal, September 2016

Plant genomics: More than food for thought journal, March 1998

Improved estimates of net primary production, growth, and standing crop of Macrocystis pyrifera in Southern California journal, August 2018

InterProScan: protein domains identifier journal, July 2005

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline journal, October 2013

Macroalgal Spore Dispersal in Coastal Environments: Mechanistic Insights Revealed by Theory and Experiment journal, November 2006

Importance of Seaweeds and Extractive Species in Global Aquaculture Production journal, September 2020

Ab initio Gene Finding in Drosophila Genomic DNA journal, April 2000

Insight into the genome data of commercially important giant kelp Macrocystis pyrifera journal, June 2022

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome journal, March 2017

First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies journal, February 2020

Circos: An information aesthetic for comparative genomics journal, June 2009

Development of PCR‐Based Markers to Determine the Sex of Kelps journal, October 2015

A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem journal, July 2019

Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta) journal, January 2011

Comparative Receptor Study in Gamete Chemotaxis of the Seaweeds Ectocarpus siliculosus and Cutleria multifida. An Approach to Interspecific Communication of Algal Gametes journal, July 1983

Role of Settlement Density on Gametophyte Growth and Reproduction in the Kelps Pterygophora Californica and Macrocystis Pyrifera (Phaeophyceae)1 journal, June 1991

A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. journal, September 2014

An evaluation of methodology to determine algal genome completeness journal, October 2020

BUSCO: Assessing Genomic Data Quality and Beyond journal, December 2021

PhycoCosm, a comparative algal genomics resource journal, October 2020

Physical–biological coupling in spore dispersal of kelp forest macroalgae journal, August 2004

Sporophyte Stage Genes Exhibit Stronger Selection Than Gametophyte Stage Genes in Haplodiplontic Giant Kelp journal, January 2022

A Physically Based Model of Macroalgal Spore Dispersal in the wave and Current-Dominated Nearshore journal, May 2002

From genomics to chemical genomics: new developments in KEGG journal, January 2006

Genetic improvement of macroalgae: status to date and needs for the future journal, December 2012

Evolution of Macrocystis spp. (Phaeophyceae) as Determined by its1 and its2 Sequences1, journal, August 2001

Full-length transcriptome assembly from RNA-Seq data without a reference genome journal, May 2011

Fast and accurate long-read alignment with Burrows–Wheeler transform journal, January 2010

Seaweed cultivation: potential and challenges of crop domestication at an unprecedented pace journal, January 2015

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast journal, January 2017

Fast and sensitive protein alignment using DIAMOND journal, November 2014

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions journal, November 2013

Saccharina genomes provide novel insight into kelp biology journal, April 2015

The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses journal, May 2021

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom journal, July 2016

Current challenges to virus discovery by meta-transcriptomics journal, December 2021

KMC 3: counting and manipulating k-mer statistics journal, May 2017

Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific journal, September 2015

The Usages and Potential Uses of Alginate for Healthcare Applications journal, October 2021

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome journal, October 2009

SAMBLASTER: fast duplicate marking and structural variant read extraction journal, May 2014

GeneWise and Genomewise journal, May 2004

UniProt: the universal protein knowledgebase in 2021 journal, November 2020

A high-performance computing toolset for relatedness and principal component analysis of SNP data journal, October 2012

Spore Supply and Habitat Availability as Sources of Recruitment Limitation in the Giant kelp Macrocystis Pyrifera (Phaeophyceae)1 journal, March 2004

Nuclear DNA Content Variation in Different Life Cycle Stages of Sugar Kelp, Saccharina latissima journal, July 2022

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation journal, March 2017

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks journal, September 2012

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs journal, March 2023

The genome atlas: navigating a new era of reference genomes journal, September 2021

Connectivity structures local population dynamics: a long-term empirical test in a large metapopulation system journal, December 2015

Minimap2: pairwise alignment for nucleotide sequences journal, May 2018

A comparative evaluation of genome assembly reconciliation tools journal, May 2017

The Ectocarpus genome and the independent evolution of multicellularity in brown algae journal, June 2010

De novo identification of repeat families in large genomes journal, June 2005

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype journal, August 2019

RepeatModeler2 for automated genomic discovery of transposable element families journal, April 2020

The variant call format and VCFtools journal, June 2011

An effective DNA extraction protocol for brown algae journal, June 2001

Fungal Genomics book, May 2014

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping journal, December 2014

Estimating the Repeat Structure and Length of DNA Sequences Using ℓ-Tuples journal, August 2003

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training journal, October 2008

Reliability Measures for Membrane Protein Topology Prediction Algorithms journal, March 2003

The role of Reproductive Synchrony in the Colonization Potential of kelp journal, December 1997

Fast and accurate de novo genome assembly from long uncorrected reads journal, January 2017

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
journal, January 1997

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.
journal, November 2015

Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)
journal, June 2020

QUAST: quality assessment tool for genome assemblies
journal, February 2013

Nuclear DNA level and life cycle of kelps: Evidence for sex-specific polyteny in Macrocystis (Laminariales, Phaeophyceae)
journal, January 2016

Unexpected cross-species contamination in genome sequencing projects
journal, January 2014

A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida
journal, January 2021

Seaweed breeding programs and progress in eastern Asian countries
journal, September 2019

Breeding, economic traits evaluation, and commercial cultivation of a new Saccharina variety “Huangguan No. 1”
journal, April 2014

The Effects of Variable Settlement and Early Competition on Patterns of Kelp Recruitment
journal, April 1990

Scaling up bioethanol production from the farmed brown macroalga Macrocystis pyrifera in Chile: Kelp based bioethanol production
journal, September 2016

Plant genomics: More than food for thought
journal, March 1998

Improved estimates of net primary production, growth, and standing crop of Macrocystis pyrifera in Southern California
journal, August 2018

InterProScan: protein domains identifier
journal, July 2005

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
journal, October 2013

Macroalgal Spore Dispersal in Coastal Environments: Mechanistic Insights Revealed by Theory and Experiment
journal, November 2006

Importance of Seaweeds and Extractive Species in Global Aquaculture Production
journal, September 2020

Ab initio Gene Finding in Drosophila Genomic DNA
journal, April 2000

Insight into the genome data of commercially important giant kelp Macrocystis pyrifera
journal, June 2022

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
journal, March 2017

First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies
journal, February 2020

Circos: An information aesthetic for comparative genomics
journal, June 2009

Development of PCR‐Based Markers to Determine the Sex of Kelps
journal, October 2015

A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem
journal, July 2019

Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta)
journal, January 2011

Comparative Receptor Study in Gamete Chemotaxis of the Seaweeds Ectocarpus siliculosus and Cutleria multifida. An Approach to Interspecific Communication of Algal Gametes
journal, July 1983

Role of Settlement Density on Gametophyte Growth and Reproduction in the Kelps Pterygophora Californica and Macrocystis Pyrifera (Phaeophyceae)1
journal, June 1991

A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp.
journal, September 2014

An evaluation of methodology to determine algal genome completeness
journal, October 2020

BUSCO: Assessing Genomic Data Quality and Beyond
journal, December 2021

PhycoCosm, a comparative algal genomics resource
journal, October 2020

Physical–biological coupling in spore dispersal of kelp forest macroalgae
journal, August 2004

Sporophyte Stage Genes Exhibit Stronger Selection Than Gametophyte Stage Genes in Haplodiplontic Giant Kelp
journal, January 2022

A Physically Based Model of Macroalgal Spore Dispersal in the wave and Current-Dominated Nearshore
journal, May 2002

From genomics to chemical genomics: new developments in KEGG
journal, January 2006

Genetic improvement of macroalgae: status to date and needs for the future
journal, December 2012

Evolution of Macrocystis spp. (Phaeophyceae) as Determined by its1 and its2 Sequences1,
journal, August 2001

Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010

Seaweed cultivation: potential and challenges of crop domestication at an unprecedented pace
journal, January 2015

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
journal, January 2017

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
journal, November 2013

Saccharina genomes provide novel insight into kelp biology
journal, April 2015

The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses
journal, May 2021

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
journal, July 2016

Current challenges to virus discovery by meta-transcriptomics
journal, December 2021

KMC 3: counting and manipulating k-mer statistics
journal, May 2017

Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific
journal, September 2015

The Usages and Potential Uses of Alginate for Healthcare Applications
journal, October 2021

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
journal, October 2009

SAMBLASTER: fast duplicate marking and structural variant read extraction
journal, May 2014

GeneWise and Genomewise
journal, May 2004

UniProt: the universal protein knowledgebase in 2021
journal, November 2020

A high-performance computing toolset for relatedness and principal component analysis of SNP data
journal, October 2012

Spore Supply and Habitat Availability as Sources of Recruitment Limitation in the Giant kelp Macrocystis Pyrifera (Phaeophyceae)1
journal, March 2004

Nuclear DNA Content Variation in Different Life Cycle Stages of Sugar Kelp, Saccharina latissima
journal, July 2022

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
journal, March 2017

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
journal, September 2012

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs
journal, March 2023

The genome atlas: navigating a new era of reference genomes
journal, September 2021

Connectivity structures local population dynamics: a long-term empirical test in a large metapopulation system
journal, December 2015

Minimap2: pairwise alignment for nucleotide sequences
journal, May 2018

A comparative evaluation of genome assembly reconciliation tools
journal, May 2017

The Ectocarpus genome and the independent evolution of multicellularity in brown algae
journal, June 2010

De novo identification of repeat families in large genomes
journal, June 2005

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
journal, August 2019

RepeatModeler2 for automated genomic discovery of transposable element families
journal, April 2020

The variant call format and VCFtools
journal, June 2011

An effective DNA extraction protocol for brown algae
journal, June 2001

Fungal Genomics
book, May 2014

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
journal, December 2014

Estimating the Repeat Structure and Length of DNA Sequences Using ℓ-Tuples
journal, August 2003

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
journal, October 2008

Reliability Measures for Membrane Protein Topology Prediction Algorithms
journal, March 2003

The role of Reproductive Synchrony in the Colonization Potential of kelp
journal, December 1997

Fast and accurate de novo genome assembly from long uncorrected reads
journal, January 2017

The Sequence Alignment/Map format and SAMtools
journal, June 2009

Intraindividual Variation in Nuclear DNA Content in Durvillaea Antarctica (Chamisso) Hariot, Macrocystis pyrifera (Linnaeus) C. Agardh and Lessonia spicata (Suhr) Santelices (Phaeophyceae)
journal, March 2019

MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013