Publications

2021

A chromosomal assembly of the soybean cyst nematode genome
Masonbrink R, et al., Mol Ecol Resour., 2021, October

Rootstocks influence the response of ripening grape berries to leafroll associated viruses
Vondras AM, et al., Mol Plant Pathol, 2021, August

Chromosomal-level genome assembly of the painted sea urchin Lytechinus pictus, a genetically enabled model system for cell biology and embryonic development
Warner JF, et al., Genome Biology and Evolution, 2021, April 5

Towards complete and error-free genome assemblies of all vertebrate species
Rhie A, et al., Nature, 2021, April

Widespread recombination suppression facilitates plant sex chromosome evolution
Rifkin JL, et al., Mol Biol Evol., 2021, March 9

Chromosome-scale, haplotype-resolved assembly of human genomes
Garg S, et al., Nature biotechnology, 2021, March

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
Liu J, et al., Genome Research, 2021, March

Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn
Hu Y, et al., Nature communications, 2021, February 23

Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes
Bedoya AM, Leaché AD,, G3 (Bethesda), 2021, February 9

Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan
Burley JT, et al., G3 (Bethesda), 2021, February 9

Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus
Guerrero FD, et al., Data in Brief, 2021, February 6

Structural and Functional Genomics of Chenopodium quinoa
Rey E, Jarvis DE,, The Quinoa Genome, 2021, February 5

Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers
Baiz MD, et al., Current Biology, 2021, February

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication
Nong W, et al., Communications Biology, 2021, January 19

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina
Friis G, et al., G3 (Bethesda), 2021, January 18

Insights from the first genome assembly of Onion (Allium cepa)
Finkers R, et al., bioRxiv, 2021, January 1

De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements
Pootakham W, et al., Molecular Ecology Resources, 2021, January

A chromosome‐scale assembly of the black gram (Vigna mungo) genome
Pootakham W, et al., Molecular Ecology Resources, 2021, January

2020

A low‐cost pipeline for soil microbiome profiling
Bollmann‐Giolai A, et al., MicrobiologyOpen, 2020, December

A Reference Genome Sequence for Giant Sequoia
Scott AD, et al., G3: Genes, Genomes, Genetics, 2020, November 5

A comparative genomics multitool for scientific discovery and conservation
Zoonomia Consortium,, Nature, 2020, November

Integrating genomics into conservation management
Latch EK; , Molecular ecology resources, 2020, November

Dense sampling of bird diversity increases power of comparative genomics
Feng S, et al., Nature, 2020, November

Genome biology of the paleotetraploid perennial biomass crop Miscanthus
Mitros T, et al., Nature communications, 2020, October 28

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra
Winter S, et al., Gigabyte, 2020, October 20

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome
Li Y, et al., BMC genomics, 2020, October 15

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Harrop TWR, et al., G3: Genes, Genomes, Genetics, 2020, October 5

“Mind the Gap”: Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions
Acquadro A, et al., G3: Genes, Genomes, Genetics, 2020, October 5

Millipede genomes reveal unique adaptations during myriapod evolution
Qu Z, et al., PLoS biology, 2020, September 29

Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding
Kadota M, et al., Scientific reports, 2020, September 3

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Mudd AB, et al., Communications biology, 2020, September 1

Advances in genomics of cashew tree: molecular tools and strategies for accelerated breeding
Savadi S, Muralidhara BM, Preethi P,, Tree Genetics & Genomes, 2020, August 5

Discovery and population genomics of structural variation in a songbird genus
Weissensteiner M, et al., Nature communications, 2020, July 7

Chromosomal‐level reference genome of the incense tree Aquilaria sinensis
Nong W, et al., Molecular ecology resources, 2020, July

Harnessing genomics to fast-track genetic improvement in aquaculture
Houston RD, et al., Nature Reviews Genetics, 2020, July

Analysis of global patents for the trend of synthetic biology inventions
Daming C, et al., Synthetic Biology Journal, 2020, June 30

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing
Nong W, et al., Nature communications, 2020, June 19

A genome assembly of the barley ‘transformation reference’cultivar golden promise
Schreiber M, et al., G3: Genes, Genomes, Genetics, 2020, June 1

Deeply conserved synteny resolves early events in vertebrate evolution
Simakov O, et al., Nature ecology & evolution, 2020, June

Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation
Tigan, A, et al., Genome Biol Evol., 2020, June

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes
Uengwetwanit T, et al., bioRxiv [pre-print], 2020, May 16

The genomics of Cannabis and its close relatives
Kovalchuk I, et al., Annual review of plant biology, 2020, April 29

A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions
Masonbrink R, et al., PLoS One, 2020, April 28

A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia
Louha S, et al., G3: Genes, Genomes, Genetics, 2020, April 9

A genome assembly of the barley ‘transformation reference’ cultivar Golden Promise
Schreiber M, et al., G3: Genes, Genomes, Genetics. , 2020, April 3

Molluscan genomics: the road so far and the way forward
Gomes-dos-Santos A, et al., Hydrobiologia, 2020, April

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization
Teterina AA, Willis JH, Phillips PC,, Genetics, 2020, April

De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen BD, et al., GigaScience., 2020, March 19

Chromosomal‐level reference genome of the incense tree Aquilaria sinensis
Nong W, et al.,  Molecular Ecology Resources., 2020, March 10

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization
Teterina AA, et al., Genetics., 2020, February 28

Characterization of a large pericentric inversion in Plateau Fence Lizards,(Sceloporus tristichus): evidence from chromosome-scale genomes
Bedoya, AM, Leaché AD,, G3 (Bethesda), 2020, February 11

Widespread recombination suppression facilitates plant sex chromosome evolution
Rifkin JL, et al., bioRxiv [pre-print], 2020, February 7

Discovery of a new TLR gene and gene expansion event through improved desert tortoise genome assembly with chromosome-scale scaffolds
Dolby GA, et al., Genome biology and evolution, 2020, February 1

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes
Bray MS, et al., Environmental microbiology reports, 2020, February

DoveTail Genomics-Advances in De Novo Genome Assembly with Dovetail Genomics–Methods, Applications, and Some Pretty Cool Science!
Holder N,, Plant and Animal Genome XXVIII Conference, 2020, January 15

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data
Armstrong EE, et al., BMC biology, 2020, January 8

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins
Suryamohan S, et al., Nature Genetics., 2020, January 6

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia
Wang B, et al., bioRxiv, 2020, January 1

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference
Wang C, et al., bioRxiv, 2020, January 1

Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly
Johnson HA, et al., bioRxiv, 2020, January 1

A Solanum lycopersicoides reference genome facilitates biological discovery in tomato
Powell AF, et al., BioRxiv, 2020, January 1

The giant sequoia genome and proliferation of disease resistance genes
Scott AD, et al., bioRxiv, 2020, January 1

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae
Ghosh A, et al., Genome Biol Evol., 2020, January 1

A draft genome sequence of the elusive giant squid, Architeuthis dux
da Fonseca RR, et al., GigaScience. , 2020, January 1

Accurate chromosome-scale haplotype-resolved assembly of human genomes
Garg S, et al., bioRxiv, 2020, January

2019

Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel
Grabek KR, et al., Communications Biology., 2019, December 20

Dichotomy of dosage compensation along the neo Z chromosome of the monarch butterfly
Gu L, et al., Current Biology. , 2019, December 2

A highly contiguous reference genome for northern bobwhite (Colinus virginianus)
Salter JF, et al., G3 (Bethesda), 2019, December 1

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species
Maughan PJ, et al., BMC Biology, 2019, November 22

Towards an adaptive and genomic understanding of an exaggerated secondary sexual trait in water striders
Toubiana W, Biodiversity. Université de Lyon, 2019, November 12

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
Burkhardt AK, et al., BMC Genomics, 2019, November 4

Genome sequence and analysis of the eggplant (Solanum melongena L.)
Li D, et al., bioRxiv [pre-print], 2019, October 31

The major histocompatibility complex of old world camels-a synopsis
Plasil M, et al., Cells, 2019, October 5

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
Kuon J, et al., BMC Biology, 2019, September 18

Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition
Kalbfleisch TS, et al., Nature Communications, 2019, September 11

Old world camels in a modern world – a balancing act between conservation and genetic improvement
Burger PA, et al., Animal Genetics. , 2019, September 18

The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters
van Hoek ML, et al., BMC Genomics, 2019, August 30

De novo genome sequence assembly of dwarf coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) provides insights into genomic variation between coconut types and related palm species
Lantican DV, et al., G3 (Bethesda), 2019, August 9

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)
Farre M, et al., GigaScience, 2019, July 30

The caribou (Rangifer tarandus) genome
Taylor RS, et al., Genes, 2019, July 17

A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality
Carballo J, et al., Scientific Reports., 2019, July 15

Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary
Elbers JP, et al., Mol Ecol Resour., 2019, July

Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids
Richardson MF, et al., Front. Genet, 2019, June 21

Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter
Beichman AC, et al., Molecular Biology and Evolution. , 2019, June 18

Gene family evolution in the pea aphid based on chromosome-level genome asssembly
Lin Y, et al., Molecular Biology and Evolution. , 2019, June 7

Modern technologies and algorithms for scaffolding assembled genomes
Ghurye J, Pop M, PLOS Computational Biology, 2019, June 5

The draft genome of eggplant
Hirakawa H, The Eggplant Genome, 2019, May 31

Structural variation detection by proximity ligation from formalin-fixed, paraffin-embedded tumor tissue
Troll CJ, et al., J Mol Diagn, 2019, May

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary
Elbers JP, et al., Molecular Ecology Resources, 2019, April 11

Origin and evolution of the octoploid strawberry genome
Edgar PP, et al., Nat Genet., 2019, April

A reference-grade wild soybean genome
Xie M, et al., Nature Communications. , 2019, March 14

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Colle M, et al., GigaScience, 2019, March 1

A critical comparison of technologies for a plant genome sequencing project
Paajanen P, et al., GigaScience, 2019, March

The new bovine reference genome assembly provides new insight into genomic organization of the bovine major histocompatibility complex
Zorc M, et al., Journal of Central European Agriculture, 2019, March

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
Belcaid M, et al., PNAS, 2019, February 19

New approaches for genome assembly and scaffolding
Rice ES, Green RE. , Annu Rev Anim Biosci., 2019, February 15

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Low WY, et al., Nature Communications., 2019, January 16

2018

Comparative analysis of the Pocillopora damiconis genome highlights roles of immune system in coral evolution
Cunning R, et al., Scientific Reports., 2018, October 31

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
Lilue J, et al., Nature Genetics., 2018, October 1

The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants
Nallu S, et al., Nature Ecology & Evolution, 2018, September

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves 
Powell D, et al., DNA Research, 2018, August 31

Chicago® and Dovetail™ Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome
Nuss AB, et al., bioRxiv [pre-print], 2018, August 15

High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)
Autenrieth M, et al., Molecular Ecology Resources, 2018, July 23

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution
Chaw SM, et al., bioRxiv [pre-print], 2018, July 18

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars
Thind AK, et al.,  BMC Genome Biology, 2018, July 10

Decimation by sea star wasting disease and rapid genetic change in keystone species, Pisaster ochracceus 
Schiebelhut LM, et al., Proc Natl Acad Sci U S A, 2018, July 3

A high-quality reference genome for the invasive mosquitofish Gambusia affinis using a chicago library
Hoffberg SL, et al., G3 (Bethesda)., 2018, May 31

The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes
Denton RD, et al., bioRxiv [pre-print], 2018, May 24

Improved genome assembly and annotation for the rock pigeon (Columba livia)
Holt C, et al., G3 (Bethesda). , 2018, May 4

Improved de novo genomic assembly for the domestic donkey
Renaud G, et al., Sci Rep., 2018, April 4

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
Medoza MLZ, et al., Nat Ecol Evol, 2018, April

EquCab3, an updated reference genome for the domestic horse
Kalbfleisch TS, et al., bioRxiv [pre-print], 2018, April

The sea lamprey germline provides insights into programmed genome rearrangements and vertebrate evolution
Smith JJ, et al., Nat Genet., 2018, February

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
Fernandez-Silva I, et al., Sci Rep. , 2018, January 28

2017

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
Kuderna LFK, et al., Sci Rep., 2017, November 1

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
Moll KM, et al., BMC Genomics, 2017, August 14

The impact of third generation genomic technologies on plant genome assembly
Thind AK, et al., Nat Biotechnol. , 2017, August

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Schwager EE, et al., BMC Biol, 2017, July 31

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Rice ES, et al., Genome Res. , 2017, May

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
Jiao WB, et al., Genome Res., 2017, May

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Reyes-Chin-Wo S, et al., Nat Commun., 2017, April 12

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Laio WB, Schneeberger K, Current Opinion in Plant Biology, 2017, April

The genome of Chenopodium quinoa
Jarvis DE, et al., Nature, 2017, February 16

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
Pootakham W, et al., Sci Rep, 2017, February 2

The draft genome of tropical fruit durian (Durio zibethinus)
Teh BT, et al., Nat Genet, 2017, November

2016