Welcome to diArk 3.0.

B. Hammesfahr, F. Odronitz, M. Hellkamp & M. Kollmar (2011) diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data. BMC Research Notes 4, 338.

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Fusarium oxysporum f. sp. lycopersici Fol029

Courtesy of Magnus Gammelgaard

Taxonomy: Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Pezizomycotina | leotiomyceta | sordariomyceta | Sordariomycetes | Hypocreomycetidae | Hypocreales | Nectriaceae | Fusarium | Fusarium oxysporum species complex | Fusarium oxysporum Comment: plant pathogen Go to NCBI Taxonomy (59765) Encyclopedia of life Wikipedia Projects: National Center for Biotechnology Information: NCBI Fungi Genomes Project Publication: van Dam P, Fokkens L, Schmidt SM et. al. (2016) Effector profiles distinguish formae speciales of Fusarium oxysporum. Environ Microbiol 18, 4087-4102. 10.1111/1462-2920.13445

Newest Species and Genome Assemblies in diArk

2018-10-15

Kluyveromyces marxianus LHW O v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Saccharomycetaceae | Kluyveromyces
Coverage: 812 | Contigs: 479 | GC-Content: 40.1% | Bases: 10.8Mbp | Filesize: 10.47MB

Komagataella phaffii v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Phaffomycetaceae | Komagataella
Contigs: 33 | GC-Content: 41.1% | Bases: 9.3Mbp | Filesize: 9.05MB

Metschnikowia bicuspidata Baker2002 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Metschnikowiaceae | Metschnikowia
Coverage: 100 | Contigs: 488 | GC-Content: 51.1% | Bases: 10.6Mbp | Filesize: 10.29MB

Metschnikowia bicuspidata Baker2002 v.1.0.0 (supercontigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Metschnikowiaceae | Metschnikowia
Coverage: 100 | Contigs: 478 | GC-Content: 51.1% | Bases: 10.6Mbp | Filesize: 10.66MB

2018-10-12

Saccharomycodes ludwigii UTAD17 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Saccharomycodaceae | Saccharomycodes
Contigs: 1360 | GC-Content: 31.2% | Bases: 10.8Mbp | Filesize: 10.6MB

Yarrowia lipolytica NCIM 3589 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Dipodascaceae | Yarrowia
Coverage: 140 | Contigs: 375 | GC-Content: 49.0% | Bases: 20.5Mbp | Filesize: 19.83MB

Yarrowia lipolytica NCIM 3590 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Dipodascaceae | Yarrowia
Coverage: 600 | Contigs: 485 | GC-Content: 47.1% | Bases: 20.0Mbp | Filesize: 19.4MB

2018-04-20

Wickerhamiella galacta NRRL Y 17645 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Trichomonascaceae | Wickerhamiella
Coverage: 27.27 | Contigs: 2137 | GC-Content: 51.8% | Bases: 9.6Mbp | Filesize: 9.58MB

2018-04-09

Hanseniaspora sp NB 2018a CRUB 1928 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Saccharomycodaceae | Hanseniaspora
Coverage: 29.3 | Contigs: 338 | GC-Content: 37.1% | Bases: 10.1Mbp | Filesize: 9.88MB

2018-04-08

Zygosaccharomyces kombuchaensis CBS 8849 v.1.0.0 (contigs)
Taxonomy: Opisthokonta | Fungi | Dikarya | . . . | Saccharomycetaceae | Zygosaccharomyces
Coverage: 23 | Contigs: 480 | GC-Content: 44.3% | Bases: 10.0Mbp | Filesize: 9.73MB

Newest Genome Publications in diArk

Wickerhamiella galacta NRRL Y 17645 Zygosaccharomyces kombuchaensis CBS 8849

Goncalves C, Wisecaver JH, Kominek J et. al. (2018)

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.

Elife 7.

10.7554/eLife.33034

Candida glabrata FFUL887

Salazar SB, Wang C, Munsterkotter M et. al. (2018)

Comparative genomic and transcriptomic analyses unveil novel features of azole resistance and adaptation to the human host in Candida glabrata.

FEMS Yeast Res 18.

10.1093/femsyr/fox079

Saccharomycopsis fermentans CBS 7830

Hesselbart A, Junker K, Wendland J (2018)

Draft Genome Sequence of Saccharomycopsis fermentans CBS 7830, a Predacious Yeast Belonging to the Saccharomycetales.

Genome Announc 6.

10.1128/genomeA.01445-17

Diutina catenulata WY3 10 4

O'Brien CE, McCarthy CGP, Walshe AE et. al. (2018)

Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade.

PLoS One 13, e0198957.

10.1371/journal.pone.0198957

Pichia kudriavzevii SJP SNU

Hong SM, Kwon HJ, Park SJ et. al. (2018)

Genomic and probiotic characterization of SJP-SNU strain of Pichia kudriavzevii.

AMB Express 8, 80.

10.1186/s13568-018-0609-0

Peterozyma xylosa NRRL Y 12939 Nakazawaea wickerhamii NRRL Y-2563 Saturnispora dispora NRRL Y-1447 Candida boidinii NRRL Y-2332 Saccharomycopsis capsularis NRRL Y-17639 Ambrosiozyma philentoma NRRL Y-7523 Citeromyces matritensis NRRL Y-2407

Krassowski T, Coughlan AY, Shen XX et. al. (2018)

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

Nat Commun 9, 1887.

10.1038/s41467-018-04374-7

Saccharomyces uvarum U3 Saccharomyces uvarum U4 Saccharomyces uvarum U2 Saccharomyces uvarum U1

Albertin W, Chernova M, Durrens P et. al. (2018)

Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations.

Yeast 35, 141-156.

10.1002/yea.3248

Hyaena hyaena

Westbury MV, Hartmann S, Barlow A et. al. (2018)

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.

Mol Biol Evol 35, 1225-1237.

10.1093/molbev/msy037

Chlorella sorokiniana Micractinium conductrix SAG 241.80

Arriola MB, Velmurugan N, Zhang Y et. al. (2018)

Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga.

Plant J 93, 566-586.

10.1111/tpj.13789

Metschnikowia fructicola AP47 Metschnikowia fructicola 277

Piombo E, Sela N, Wisniewski M et. al. (2018)

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases.

Front Microbiol 9, 593.

10.3389/fmicb.2018.00593

Ambystoma mexicanum DD151

Nowoshilow S, Schloissnig S, Fei JF et. al. (2018)

The axolotl genome and the evolution of key tissue formation regulators.

Nature 554, 50-55.

10.1038/nature25458

Seriola lalandi dorsalis

Purcell CM, Seetharam AS, Snodgrass O et. al. (2018)

Insights into teleost sex determination from the Seriola dorsalis genome assembly.

BMC Genomics 19, 31.

10.1186/s12864-017-4403-1

Acridotheres javanicus

Low GW, Chattopadhyay B, Garg KM et. al. (2018)

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Heredity (Edinb) 120, 138-153.

10.1038/s41437-017-0026-1

Eschscholzia californica subsp californica

Hori K, Yamada Y, Purwanto R et. al. (2018)

Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence.

Plant Cell Physiol 59, 222-233.

10.1093/pcp/pcx210

Eulimnadia texana

Baldwin-Brown JG, Weeks SC, Long AD (2018)

A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome.

Genome Biol Evol 10, 143-156.

10.1093/gbe/evx280

Aspergillus niger FGSC A1279

Wang B, Lv Y, Li X et. al. (2018)

Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis.

Res Microbiol 169, 67-77.

10.1016/j.resmic.2017.10.002

Anser brachyrhynchus

Pujolar JM, Dalen L, Olsen RA et. al. (2018)

First de novo whole genome sequencing and assembly of the pink-footed goose.

Genomics 110, 75-79.

10.1016/j.ygeno.2017.08.008

Uria lomvia

Tigano A, Sackton TB, Friesen VL (2018)

Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia).

Mol Ecol Resour 18, 79-90.

10.1111/1755-0998.12712

Aspergillus arachidicola CBS 117610

Moore GG, Mack BM, Beltz SB et. al. (2018)

Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola.

BMC Genomics 19, 189.

10.1186/s12864-018-4576-2

Labrus bergylta

Lie KK, Torresen OK, Solbakken MH et. al. (2018)

Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish.

BMC Genomics 19, 186.

10.1186/s12864-018-4570-8

Trichoplusia ni

Fu Y, Yang Y, Zhang H et. al. (2018)

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.

Elife 7.

10.7554/eLife.31628

Meyerozyma caribbica

De Marco L, Epis S, Capone A et. al. (2018)

The Genomes of Four Meyerozyma caribbica Isolates and Novel Insights into the Meyerozyma guilliermondii Species Complex.

G3 (Bethesda) 8, 755-759.

10.1534/g3.117.300316

Santalum album cultivar GKVK 1

Mahesh HB, Subba P, Advani J et. al. (2018)

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome.

Plant Physiol 176, 2772-2788.

10.1104/pp.17.01764

Mus caroli Mus pahari

Thybert D, Roller M, Navarro FCP et. al. (2018)

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Genome Res 28, 448-459.

10.1101/gr.234096.117

Desmodus rotundus

Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M et. al. (2018)

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Nat Ecol Evol 2, 659-668.

10.1038/s41559-018-0476-8

Aspergillus tubingensis G131

Choque E, Klopp C, Valiere S et. al. (2018)

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

BMC Genomics 19, 200.

10.1186/s12864-018-4574-4

Blattella germanica Cryptotermes secundus

Harrison MC, Jongepier E, Robertson HM et. al. (2018)

Hemimetabolous genomes reveal molecular basis of termite eusociality.

Nat Ecol Evol 2, 557-566.

10.1038/s41559-017-0459-1

Uroleptopsis citrina UcQD2011

Zheng W, Wang C, Yan Y et. al. (2018)

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.

Genome Biol Evol 10, 883-894.

10.1093/gbe/evy055

Heterobasidion parviporum 96026

Zeng Z, Sun H, Vainio EJ et. al. (2018)

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors.

BMC Genomics 19, 220.

10.1186/s12864-018-4610-4

Planoprotostelium fungivorum

Hillmann F, Forbes G, Novohradska S et. al. (2018)

Multiple Roots of Fruiting Body Formation in Amoebozoa.

Genome Biol Evol 10, 591-606.

10.1093/gbe/evy011

Crithidia bombi Crithidia expoeki

Schmid-Hempel P, Aebi M, Barribeau S et. al. (2018)

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees.

PLoS One 13, e0189738.

10.1371/journal.pone.0189738

Talaromyces adpressus CBS 142503

Cerullo G, Houbraken J, Granchi Z et. al. (2018)

Draft Genome Sequence of Talaromyces adpressus.

Genome Announc 6, e01430-17.

10.1128/genomeA.01430-17

Magnaporthe oryzae WBKY11 Magnaporthe oryzae WHTQ Magnaporthe grisea VO107

Gladieux P, Condon B, Ravel S et. al. (2018)

Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae.

MBio 9, e01219-17.

10.1128/mBio.01219-17

Juglans mandshurica Juglans nigra Juglans regia

Bai WN, Yan PC, Zhang BW et. al. (2018)

Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences.

New Phytol 217, 1726-1736.

10.1111/nph.14917

Schmidtea mediterranea str S2

Grohme MA, Schloissnig S, Rozanski A et. al. (2018)

The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms.

Nature 554, 56-61.

10.1038/nature25473

Physcomitrella patens

Lang D, Ullrich KK, Murat F et. al. (2018)

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Plant J 93, 515-533.

10.1111/tpj.13801

Verticillium longisporum

Fogelqvist J, Tzelepis G, Bejai S et. al. (2018)

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

BMC Genomics 19, 14.

10.1186/s12864-017-4407-x

Dicerorhinus sumatrensis sumatrensis

Mays HL Jr., Hung CM, Shaner PJ et. al. (2018)

Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis.

Curr Biol 28, 70-76.e4.

10.1016/j.cub.2017.11.021

Pyrenophora teres f teres 0 1

Wyatt NA, Richards JK, Brueggeman RS et. al. (2018)

Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0-1.

G3 (Bethesda) 8, 1-8.

10.1534/g3.117.300196

Cercocebus atys

Palesch D, Bosinger SE, Tharp GK et. al. (2018)

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.

Nature 553, 77-81.

10.1038/nature25140

Notospermus geniculatus Phoronis australis

Luo YJ, Kanda M, Koyanagi R et. al. (2018)

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.

Nat Ecol Evol 2, 141-151.

10.1038/s41559-017-0389-y

Caenorhabditis nigoni JU1422

Yin D, Schwarz EM, Thomas CG et. al. (2018)

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins.

Science 359, 55-61.

10.1126/science.aao0827

Pseudogymnoascus destructans 20631 21 Pseudogymnoascus sp. 03VT05 Pseudogymnoascus sp. 05NY08 Pseudogymnoascus sp. 23342-1-I1 Pseudogymnoascus sp. 24MN13 Pseudogymnoascus sp. WSF 3629 Pseudogymnoascus verrucosus UAMH 10579

Palmer JM, Drees KP, Foster JT et. al. (2018)

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats.

Nat Commun 9, 35.

10.1038/s41467-017-02441-z

Cajanus cajan

Mahato AK, Sharma AK, Sharma TR et. al. (2018)

An improved draft of the pigeonpea (Cajanus cajan (L.) Millsp.) genome.

Data Brief 16, 376-380.

10.1016/j.dib.2017.11.066

Zygosaccharomyces bailii IST302

Palma M, Munsterkotter M, Peca J et. al. (2017)

Genome sequence of the highly weak-acid-tolerant Zygosaccharomyces bailii IST302, amenable to genetic manipulations and physiological studies.

FEMS Yeast Res 17.

10.1093/femsyr/fox025

Fusarium fujikuroi m567 Fusarium fujikuroi MRC2276 Fusarium fujikuroi C1995 Fusarium fujikuroi B14 Fusarium fujikuroi E282 Fusarium fujikuroi FSU48 Fusarium fujikuroi NCIM1100 Fusarium fujikuroi Fusarium oxysporum V64-1

Niehaus EM, Kim HK, Munsterkotter M et. al. (2017)

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles.

PLoS Pathog 13, e1006670.

10.1371/journal.ppat.1006670

Armillaria cepistipes B5 Armillaria ostoyae C18/9 Armillaria gallica 21-2 Armillaria solidipes 28-4

Sipos G, Prasanna AN, Walter MC et. al. (2017)

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.

Nat Ecol Evol 1, 1931-1941.

10.1038/s41559-017-0347-8

Spathaspora boniae UFMG CM Y306

Morais CG, Batista TM, Kominek J et. al. (2017)

Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

Int J Syst Evol Microbiol 67, 3798-3805.

10.1099/ijsem.0.002186

Zygosaccharomyces parabailii ATCC 60483

Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S et. al. (2017)

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch.

PLoS Biol 15, e2002128.

10.1371/journal.pbio.2002128

Purpose of the Database

The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective) it is therefore important to have up-to-date knowledge about the various resources providing primary data. diArk provides comprehensive search modules each with detailed options and three different views of the selected data.
To be up to date with the newest data just use our RSS-Feed on the right side.

Usage

The web interface has been designed using the next generation internet features (Web 2.0). Thus, the site makes extensive use of Ajax (Asynchronous JavaScript and XML) in order to present the user with a feature rich interface while minimizing the amount of transferred data. To use the database you therefore have to enable javascript and session-cookies.

Note

We have done our best to include all eukaryotic sequencing projects in the world that provide assembled genomic data or a considerable amount of cDNA/EST data. But we are sure that we still miss some. If you are aware of a missing project please contact us.