Assessing the gene space in draft genomes

Parra, Genis; Bradnam, Keith; Ning, Zemin; Keane, Thomas; Korf, Ian

doi:10.1093/nar/gkn916

Title: Assessing the gene space in draft genomes

Journal Article · 28 November 2008 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkn916 · OSTI ID:1625456

Parra, Genis ^[1]; Bradnam, Keith ^[2]; Ning, Zemin ^[3]; Keane, Thomas ^[3]; Korf, Ian ^[2]

Univ. of California, Davis, CA (United States). UC Davis Genome Center; DOE/OSTI
Univ. of California, Davis, CA (United States). UC Davis Genome Center
The Wellcome Trust Sanger Inst., Genome Campus, Hinxton (United Kingdom)

Genome sequencing projects have been initiated for a wide range of eukaryotes. A few projects have reached completion, but most exist as draft assemblies. As one of the main reasons to sequence a genome is to obtain its catalog of genes, an important question is how complete or completable the catalog is in unfinished genomes. To answer this question, we have identified a set of core eukaryotic genes (CEGs), that are extremely highly conserved and which we believe are present in low copy numbers in higher eukaryotes. From an analysis of a phylogenetically diverse set of eukaryotic genome assemblies, we found that the proportion of CEGs mapped in draft genomes provides a useful metric for describing the gene space, and complements the commonly used N50 length and x-fold coverage values.

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Research Organization:: University of California, Davis, CA (United States)

Sponsoring Organization:: National Human Genome Research Institute; National Institutes of Health; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI ID:: 1625456

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 1 Vol. 37; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 3 of Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires Elfstrand, Malin; Chen, Jun; Cleary, Michelle figshare https://doi.org/10.6084/m9.figshare.14905996	dataset	January 2021
Additional file 4 of Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires Elfstrand, Malin; Chen, Jun; Cleary, Michelle figshare https://doi.org/10.6084/m9.figshare.14905999	dataset	January 2021
Additional file 5 of Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires Elfstrand, Malin; Chen, Jun; Cleary, Michelle figshare https://doi.org/10.6084/m9.figshare.14906002.v1	dataset	January 2021
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De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici Aragona, Maria; Minio, Andrea; Ferrarini, Alberto BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-313	journal	January 2014
Finding the missing honey bee genes: lessons learned from a genome upgrade Elsik, Christine G.; Worley, Kim C.; Bennett, Anna K. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-86	journal	January 2014
Assessment of de novoassemblers for draft genomes: a case study with fungal genomes Abbas, Mostafa M.; Malluhi, Qutaibah M.; Balakrishnan, Ponnuraman BMC Genomics, Vol. 15, Issue S9 https://doi.org/10.1186/1471-2164-15-s9-s10	journal	December 2014
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species Bradnam, Keith R.; Fass, Joseph N.; Alexandrov, Anton GigaScience, Vol. 2, Issue 1 https://doi.org/10.1186/2047-217x-2-10	journal	July 2013
Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing Yao, Lina; Tan, Kenneth Wei Min; Tan, Tin Wee BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1551-x	journal	February 2017
Reference-guided de novo assembly approach improves genome reconstruction for related species Lischer, Heidi E. L.; Shimizu, Kentaro K. BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1911-6	journal	November 2017
FGMP: assessing fungal genome completeness Cissé, Ousmane H.; Stajich, Jason E. BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-2782-9	journal	April 2019
A comparative view of early development in the corals Favia lizardensis, Ctenactis echinata, and Acropora millepora - morphology, transcriptome, and developmental gene expression Okubo, Nami; Hayward, David C.; Forêt, Sylvain BMC Evolutionary Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12862-016-0615-2	journal	February 2016
Genomic exaptation enables Lasius niger adaptation to urban environments Konorov, Evgenii A.; Nikitin, Mikhail A.; Mikhailov, Kirill V. BMC Evolutionary Biology, Vol. 17, Issue S1 https://doi.org/10.1186/s12862-016-0867-x	journal	February 2017
Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation Gayk, Zach G.; Le Duc, Diana; Horn, Jeffrey BMC Evolutionary Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12862-018-1181-6	journal	April 2018
A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps Macrander, Jason; Brugler, Mercer R.; Daly, Marymegan BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1417-4	journal	March 2015
The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics Quandt, C. Alisha; Bushley, Kathryn E.; Spatafora, Joseph W. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1777-9	journal	July 2015
Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation de Bekker, Charissa; Ohm, Robin A.; Loreto, Raquel G. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1812-x	journal	August 2015
Gene expression underlying enhanced, steroid-dependent auditory sensitivity of hair cell epithelium in a vocal fish Fergus, Daniel J.; Feng, Ni Y.; Bass, Andrew H. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1940-3	journal	October 2015
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation Hara, Yuichiro; Tatsumi, Kaori; Yoshida, Michio BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2007-1	journal	November 2015
Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts Chan, Chai Ling; Yew, Su Mei; Ngeow, Yun Fong BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2200-2	journal	November 2015
Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum Prasad, Pushplata; Varshney, Deepti; Adholeya, Alok BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2229-2	journal	November 2015
Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis Zondag, Lisa E.; Rutherford, Kim; Gemmell, Neil J. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2435-6	journal	February 2016
Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca Giampetruzzi, Annalisa; Morelli, Massimiliano; Saponari, Maria BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2833-9	journal	June 2016
A transcriptional blueprint for a spiral-cleaving embryo Chou, Hsien-Chao; Pruitt, Margaret M.; Bastin, Benjamin R. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2860-6	journal	August 2016
Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae Han, Xiaolong; Chakrabortti, Alolika; Zhu, Jindong BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2974-x	journal	August 2016
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma Bellora, Nicolás; Moliné, Martín; David-Palma, Márcia BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3244-7	journal	November 2016
Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses Penselin, Daniel; Münsterkötter, Martin; Kirsten, Susanne BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3299-5	journal	November 2016
Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles Schlegel, Markus; Münsterkötter, Martin; Güldener, Ulrich BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3369-8	journal	December 2016
Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy Marra, Nicholas J.; Richards, Vincent P.; Early, Angela BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-016-3411-x	journal	January 2017
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod Tørresen, Ole K.; Star, Bastiaan; Jentoft, Sissel BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-016-3448-x	journal	January 2017
A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing Hoang, Nam V.; Furtado, Agnelo; Mason, Patrick J. BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3757-8	journal	May 2017
Blood meal induced regulation of the chemosensory gene repertoire in the southern house mosquito Taparia, Tanvi; Ignell, Rickard; Hill, Sharon Rose BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3779-2	journal	May 2017
Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes Conze, Lei Liu; Berlin, Sofia; Le Bail, Aude BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3972-3	journal	August 2017
Improving eukaryotic genome annotation using single molecule mRNA sequencing Magrini, Vincent; Gao, Xin; Rosa, Bruce A. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4555-7	journal	March 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 Lie, Kai K.; Tørresen, Ole K.; Solbakken, Monica Hongrø BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4570-8	journal	March 2018
New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus) Doyle, Jacqueline M.; Bell, Douglas A.; Bloom, Peter H. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4615-z	journal	April 2018
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats Tørresen, Ole K.; Brieuc, Marine S. O.; Solbakken, Monica H. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4616-y	journal	April 2018
Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots Thakur, Omika; Randhawa, Gursharn Singh BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5205-9	journal	December 2018
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata Armaleo, Daniele; Müller, Olaf; Lutzoni, François BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5629-x	journal	July 2019
Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides Pym, Adam; Singh, Kumar Saurabh; Nordgren, Åsa BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6397-3	journal	December 2019
Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats Eyres, Isobel; Boschetti, Chiara; Crisp, Alastair BMC Biology, Vol. 13, Issue 1 https://doi.org/10.1186/s12915-015-0202-9	journal	November 2015
Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes Hara, Yuichiro; Takeuchi, Miki; Kageyama, Yuka BMC Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12915-018-0509-4	journal	April 2018
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions Stephens, Timothy G.; González-Pech, Raúl A.; Cheng, Yuanyuan BMC Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12915-020-00782-8	journal	May 2020
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation Xue, Jian; Zhou, Xin; Zhang, Chuan-Xi Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0521-0	journal	December 2014
Conserved syntenic clusters of protein coding genes are missing in birds Lovell, Peter V.; Wirthlin, Morgan; Wilhelm, Larry Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0565-1	journal	December 2014
Metassembler: merging and optimizing de novo genome assemblies Wences, Alejandro Hernandez; Schatz, Michael C. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0764-4	journal	September 2015
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx Abascal, Federico; Corvelo, André; Cruz, Fernando Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1090-1	journal	December 2016
The genome of the Gulf pipefish enables understanding of evolutionary innovations Small, C. M.; Bassham, S.; Catchen, J. Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1126-6	journal	December 2016
Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages Ying, Hua; Cooke, Ira; Sprungala, Susanne Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1552-8	journal	November 2018
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes Swart, Estienne C.; Bracht, John R.; Magrini, Vincent PLoS Biology, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pbio.1001473	journal	January 2013
Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges El-Metwally, Sara; Hamza, Taher; Zakaria, Magdi PLoS Computational Biology, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pcbi.1003345	journal	December 2013
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies Denton, James F.; Lugo-Martinez, Jose; Tucker, Abraham E. PLoS Computational Biology, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pcbi.1003998	journal	December 2014
The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution Traeger, Stefanie; Altegoer, Florian; Freitag, Michael PLoS Genetics, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pgen.1003820	journal	September 2013
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes Fierst, Janna L.; Willis, John H.; Thomas, Cristel G. PLOS Genetics, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pgen.1005323	journal	June 2015
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding Vij, Shubha; Kuhl, Heiner; Kuznetsova, Inna S. PLOS Genetics, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pgen.1005954	journal	April 2016
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes Blanc-Mathieu, Romain; Perfus-Barbeoch, Laetitia; Aury, Jean-Marc PLOS Genetics, Vol. 13, Issue 6 https://doi.org/10.1371/journal.pgen.1006777	journal	June 2017
Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus Peng, Zhao; Oliveira-Garcia, Ely; Lin, Guifang PLOS Genetics, Vol. 15, Issue 9 https://doi.org/10.1371/journal.pgen.1008272	journal	September 2019
RNAi Effector Diversity in Nematodes Dalzell, Johnathan J.; McVeigh, Paul; Warnock, Neil D. PLoS Neglected Tropical Diseases, Vol. 5, Issue 6 https://doi.org/10.1371/journal.pntd.0001176	journal	June 2011
De-Novo Assembly and Analysis of the Heterozygous Triploid Genome of the Wine Spoilage Yeast Dekkera bruxellensis AWRI1499 Curtin, Chris D.; Borneman, Anthony R.; Chambers, Paul J. PLoS ONE, Vol. 7, Issue 3 https://doi.org/10.1371/journal.pone.0033840	journal	March 2012
De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana Nakasugi, Kenlee; Crowhurst, Ross N.; Bally, Julia PLoS ONE, Vol. 8, Issue 3 https://doi.org/10.1371/journal.pone.0059534	journal	March 2013
Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana Nakasugi, Kenlee; Crowhurst, Ross; Bally, Julia PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0091776	journal	March 2014
The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos) Doyle, Jacqueline M.; Katzner, Todd E.; Bloom, Peter H. PLoS ONE, Vol. 9, Issue 4 https://doi.org/10.1371/journal.pone.0095599	journal	April 2014
Transcriptome-Based Identification of Highly Similar Odorant-Binding Proteins among Neotropical Stink Bugs and Their Egg Parasitoid Farias, Luciana R.; Schimmelpfeng, Pedro H. C.; Togawa, Roberto C. PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0132286	journal	July 2015
A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis Murgarella, Maria; Puiu, Daniela; Novoa, Beatriz PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0151561	journal	March 2016
Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata Hou, Yujie; Ma, Xiao; Wan, Wenting PLOS ONE, Vol. 11, Issue 5 https://doi.org/10.1371/journal.pone.0155258	journal	May 2016
Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes Carlson, David E.; Hedin, Marshal PLOS ONE, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pone.0174102	journal	April 2017
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina Čadež, Neža; Bellora, Nicolas; Ulloa, Ricardo PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210792	journal	January 2019
Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera Wong, Barbara; Leal, Isabel; Feau, Nicolas PLOS ONE, Vol. 15, Issue 2 https://doi.org/10.1371/journal.pone.0221742	journal	February 2020
Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids Westbury, Michael V.; Petersen, Bent; Lorenzen, Eline D. PLOS ONE, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pone.0222004	journal	September 2019
Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus Kikuchi, Taisei; Cotton, James A.; Dalzell, Jonathan J. PLoS Pathogens, Vol. 7, Issue 9 https://doi.org/10.1371/journal.ppat.1002219	journal	September 2011
Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica Zuccaro, Alga; Lahrmann, Urs; Güldener, Ulrich PLoS Pathogens, Vol. 7, Issue 10 https://doi.org/10.1371/journal.ppat.1002290	journal	October 2011
Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites Wiemann, Philipp; Sieber, Christian M. K.; von Bargen, Katharina W. PLoS Pathogens, Vol. 9, Issue 6 https://doi.org/10.1371/journal.ppat.1003475	journal	June 2013
Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles Niehaus, Eva-Maria; Kim, Hee-Kyoung; Münsterkötter, Martin PLOS Pathogens, Vol. 13, Issue 10 https://doi.org/10.1371/journal.ppat.1006670	journal	October 2017
The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata Armaleo, Daniele; Müller, Olaf; Lutzoni, François BioMed Central https://doi.org/10.14288/1.0380051	text	January 2019
Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics Hooff, Jolien JE; Tromer, Eelco; Wijk, Leny M. EMBO reports, Vol. 18, Issue 9 https://doi.org/10.15252/embr.201744102	journal	June 2017
Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus ) and the Scaled Quail ( Callipepla squamata ) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size Oldeschulte, David L.; Halley, Yvette A.; Wilson, Miranda L. G3 Genes\|Genomes\|Genetics, Vol. 7, Issue 9 https://doi.org/10.1534/g3.117.043083	journal	September 2017
Genome and Ontogenetic-Based Transcriptomic Analyses of the Flesh Fly, Sarcophaga bullata Martinson, Ellen O.; Peyton, Justin; Kelkar, Yogeshwar D. G3 Genes\|Genomes\|Genetics, Vol. 9, Issue 5 https://doi.org/10.1534/g3.119.400148	journal	May 2019
Sharp switches between regular and swinger mitochondrial replication: 16S rDNA systematically exchanging nucleotides A<->T+C<->G in the mitogenome of Kamimuria wangi Seligmann, Hervé Mitochondrial DNA Part A, Vol. 27, Issue 4 https://doi.org/10.3109/19401736.2015.1033691	journal	April 2015
A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy Tang, Nianwu; San Clemente, Hélène; Roy, Sébastien Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00233	journal	March 2016
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00238	journal	March 2016
Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion Cooper, Joshua T.; Sinclair, Geoffrey A.; Wawrik, Boris Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00639	journal	May 2016
Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum Massonnet, Mélanie; Morales-Cruz, Abraham; Minio, Andrea Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01784	journal	August 2018
A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105 Iwasaka, Hiroaki; Koyanagi, Ryo; Satoh, Ryota Genes, Vol. 9, Issue 4 https://doi.org/10.3390/genes9040200	journal	April 2018
The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly Clouse, J. W.; Adhikary, D.; Page, J. T. The Plant Genome, Vol. 9, Issue 1 https://doi.org/10.3835/plantgenome2015.07.0062	journal	March 2016
The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly [Errata] The Plant Genome, Vol. 9, Issue 3 https://doi.org/10.3835/plantgenome2015.07.0062er	journal	November 2016
Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles Markus, Schlegel,; Martin, Münsterkötter,; Ulrich, Güldener, ETH Zurich https://doi.org/10.3929/ethz-b-000124732	text	January 2016
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle Aranda, Manuel; Li, Yong; Liew, Yi J. ETH Zurich https://doi.org/10.3929/ethz-b-000124876	text	January 2016
Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria György, Sipos,; N., Prasanna, Arun; C., Walter, Mathias ETH Zurich https://doi.org/10.3929/ethz-b-000207196	text	January 2017
Reference-guided de novo assembly approach improves genome reconstruction for related species Lischer, Heidi E. L.; Shimizu, Kentaro K. BioMed Central https://doi.org/10.5167/uzh-141932	text	January 2017
Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns Mikheyev, Alexander S.; Linksvayer, Timothy A. eLife, Vol. 4 https://doi.org/10.7554/elife.04775	journal	January 2015
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing Martinez Barrio, Alvaro; Lamichhaney, Sangeet; Fan, Guangyi eLife, Vol. 5 https://doi.org/10.7554/elife.12081	journal	May 2016
A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem Rabe, Franziska; Bosch, Jason; Stirnberg, Alexandra eLife, Vol. 5 https://doi.org/10.7554/elife.20522	journal	November 2016
Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano Grudniewska, Magda; Mouton, Stijn; Simanov, Daniil eLife, Vol. 5 https://doi.org/10.7554/elife.20607	journal	December 2016
Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles Schlegel, Markus; Münsterkötter, Martin; Güldener, Ulrich BioMed Central https://doi.org/10.7892/boris.98176	text	January 2016
Pan genome of the phytoplankton Emiliania underpins its global distribution Read, Betsy A.; Kegel, Jessica; Klute, Mary J. Columbia University https://doi.org/10.7916/d8nv9q13	text	January 2013
Pan genome of the phytoplankton Emiliania underpins its global distribution Read, Betsy A.; Kegel, Jessica; Klute, Mary J. Columbia University https://doi.org/10.7916/d8zc82bv	text	January 2013

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