Please cite this for EvidentialGene RNA assemblies and methods (EvigeneR): Gilbert, Donald (2013) Gene-omes built from mRNA seq not genome DNA. 7th annual arthropod genomics symposium. Notre Dame. http://arthropods.eugenes.org/EvidentialGene/about/EvigeneRNA2013poster.pdf and http://globalhealth.nd.edu/7th-annual-arthropod-genomics-symposium/ and doi:10.7490/f1000research.1112594.1 Please cite this for EvidentialGene genome-gene construction methods (EvigeneD): Gilbert, Donald (2012) Perfect Arthropod Genes constructed with Gigabases of RNA 6th annual Arthropod Genomics Symposium. Kansas State U. http://arthropods.eugenes.org/EvidentialGene/about/PerfectGenes2012poster.pdf and doi:10.7490/f1000research.1112595.1 Recent Gilbert, DG. (2022). Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants. bioRxiv; doi: 10.1101/2022.05.13.491861 Gilbert, DG. (2019). Longest protein, longest transcript or most expression, for accurate gene reconstruction of transcriptomes? bioRxiv 829184; doi: 10.1101/829184 Gilbert, DG. (2019). Genes of the Pig, Sus scrofa, reconstructed with EvidentialGene. PeerJ 7:e6374; doi:10.7717/peerj.6374 or BioRxiv, Sep 2018. doi: 10.1101/412130 -- with description of EvidentialGene omnibus SRA2Genes pipeline. Gilbert D. (2016) Accurate & complete gene construction with EvidentialGene. Talk at Galaxy Community Conference 2016, Bloomington IN. F1000Research, 5:1567 (slide set). doi:10.7490/f1000research.1112467.1; talk video: https://youtu.be/Lu4JqZPGKW0 http://eugenes.org/EvidentialGene/about/evigene_bothgalmod1606iu.pdf (full slide set) EvidentialGene is used by others in these reports Nakasugi K, Crowhurst R, Bally J, Waterhouse P (2014). Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana. PLoS ONE 9(3): e91776. doi:10.1371/journal.pone.0091776 * independent review/comparison of Evigene and other gene assembly methods * Shu Chen, J. Scott McElroy, Fenny Dane, and Eric Peatman (2014). Optimizing Transcriptome Assemblies for Eleusine indica Leaf and Seedling by Combining Multiple Assemblies from Three De Novo Assemblers. The Plant Genome, v8. doi:10.3835/plantgenome2014.10.0064 * independent review/comparison of Evigene and other gene assembly methods * Mamrot J, R Legaie, SJ. Ellery, T Wilson, T Seemann, DR. Powell, DK. Gardner, DW. Walker, P Temple-Smith, AT. Papenfuss & H Dickinson (2017). De novo transcriptome assembly for the spiny mouse (Acomys cahirinus) Scientific Reports 7, A# 8996; doi:10.1038/s41598-017-09334-7 ; also bioRxiv preprint Sep. 2016; doi: 10.1101/076067. * independent review/comparison of Evigene and other gene assembly methods * Hoang NV, A Furtado, PJ Mason, A Marquardt, L Kasirajan, PP Thirugnanasambandam, FC Botha and RJ Henry (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. BMC Genomics 18:395; doi: 10.1186/s12864-017-3757-8 * independent comparison of Pac-Bio RNA versus Illumina RNA * over-assemblies, with Evigene reduction. See comment below. Chagne D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, et al. (2014). The Draft Genome Sequence of European Pear (Pyrus communis L. Bartlett). PLoS ONE 9(4): e92644. doi:10.1371/journal.pone.0092644 Horn F, Uzum Z, Mobius N, Guthke R, Linde J, Hertweck C. (2015). Draft genome sequences of symbiotic and nonsymbiotic Rhizopus microsporus strains CBS 344.29 and ATCC 62417. Genome Announc. 3(1):e01370-14. doi:10.1128/genomeA.01370-14. Postnikova OA, Hult M, Shao J, Skantar A, Nemchinov LG (2015). Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root-Knot Nematode Meloidogyne incognita. PLoS ONE 10(2):e0118269. doi:10.1371/journal.pone.0118269 Liu Y, Lin-Wang K, Deng C, Warran B, Wang L, Yu B, et al. (2015). Comparative Transcriptome Analysis of White and Purple Potato to Identify Genes Involved in Anthocyanin Biosynthesis. PLoS ONE 10(6):e0129148. doi:10.1371/journal.pone.0129148 McTaggart SJ, Hannah T, Bridgett S, Garbutt JS, Kaur G, Boots M. (2015). Novel insights into the insect trancriptome response to a natural DNA virus. BMC Genomics. Apr 17;16(1):310. PubMed PMID:25924671; doi: 10.1186/s12864-015-1499-z Duncan, R. P., Husnik, F., Van Leuven, J. T., Gilbert, D. G., Davalos, L. M., McCutcheon, J. P. and Wilson, A. C. C. (2014). Dynamic recruitment of amino acid transporters to the insect/symbiont interface. Molecular Ecology, 23: 1608-1623. doi:10.1111/mec.12627 Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Marien J, etal. (2015). Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS ONE 10(6): e0130600. doi:10.1371/journal.pone.0130600 Lynch, Jeremy A (2015). The Expanding Genetic Toolbox of the Wasp Nasonia vitripennis and Its Relatives. Genetics, Vol. 199, 897-904, doi:10.1534/genetics.112.147512 Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S (2015). Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics,16:1057; doi:10.1186/s12864-015-2277-7 http://www.biomedcentral.com/1471-2164/16/1057 # Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander A. Myburg and Sanushka Naidoo Scott, A. D., Stenz, N. W. M., Ingvarsson, P. K. and Baum, D. A. (2016). Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers. New Phytol. doi:10.1111/nph.13930 ; bioRxiv preprint, 2015 Nov; doi:10.1101/030585 Chen, Shu; McElroy, J. Scott; Dane, Fenny; Goertzen, Leslie R. (2015). Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth. The Plant Genome; doi:10.3835/plantgenome2015.06.0050 Luo H, Xiao S, Ye H, Zhang Z, Lv C, Zheng S, et al. (2016). Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti [fish]. PLoS ONE 11(3): e0152572. doi:10.1371/journal.pone.0152572 Franta Z, Vogel H, Lehmann R, Rupp O, Goesmann A, and Vilcinskas A. (2016). Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. BioMed Research International, vol.2016, ID 8285428, 27p. doi:10.1155/2016/8285428 -- methods 2.4. Assembly: trinity + velvet/oases > EvidentialGene pipeline [51]. Wu C, Crowhurst RN, Dennis AB, Twort VG, Liu S, Newcomb RD, et al. (2016). De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction. PLoS ONE 11(6): e0157783. doi:10.1371/journal.pone.0157783 Drabesova J, Cerna L, Masterova H, Kolouskova P, Potocky M, Storchova H. (2016). The evolution of the FT/TFL1 genes in Amaranthaceae and their expression patterns in the course of vegetative growth and flowering in Chenopodium rubrum. G3: Genes|Genomes|Genetics, 2016 Oct 13;6(10):3065-3076. doi:10.1534/g3.116.028639 Huylmans A K , A L Ezquerra, J Parsch, and M Cordellier (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biol Evol doi: 10.1093/gbe/evw221 Arvidson, Ryan Scott. (2016). Venomics and Functional Analysis of Venom From the Emerald Jewel Wasp, Ampulex compressa. UC Riverside: Biochemistry and Molecular Biology. http://escholarship.org/uc/item/1ww2p6mk Healy TM, Bryant HJ, Schulte PM (2016). Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish. Molecular Ecology, online 2016/12. doi: 10.1111/mec.13945 Data from: .., Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sg280 -- use gene models of Fundulus heteroclitus from EvidentialGene/killifish/ Nguyen TV, Jung H, Nguyen TM, Hurwood D, Mather P. (2016). Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach. Mar Genomics. 2016 Feb;25:75-88. doi: 10.1016/j.margen.2015.11.010. PubMed PMID: 26653845. -- nice application of rna overassembly and reduction to accurate gene set for a fish Sales G, Deagle BE, Calura E, Martini P, Biscontin A, De Pitta C, Kawaguchi S, Romualdi C, Meyer B, Costa R, Jarman S (2017). KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PLoS ONE 12(2): e0171908. doi:10.1371/journal.pone.0171908 Voelckel C, Gruenheit N, Lockhart P (2017). Evolutionary Transcriptomics and Proteomics: Insight into Plant Adaptation. Trends in Plant Science, ISSN 1360-1385, doi:10.1016/j.tplants.2017.03.001 Roberts, W. R., & Roalson, E. H. (2017). Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics, 18, 240. doi: 10.1186/s12864-017-3623-8 Christodoulides N, Van Dam AR, Peterson DA, Frandsen RJN, Mortensen UH, Petersen B, Rasmussen S, Normark BB, Hardy NB. (2017). Gene expression plasticity across hosts of an invasive scale insect species. PLoS ONE 12(5): e0176956. doi:10.1371/journal.pone.0176956 Zinkgraf M, Gerttula S, Groover A (2017). Transcript profiling of a novel plant meristem, the monocot cambium. J Integr Plant Biol XX: 1a14; doi:10.1111/jipb.12538 -- 2 non-tree (yucca,..) + 2 tree species, trinity-only assembly :( , tr2aacds to reduce Wu, R, T Wang, B A.W. Warren, A C. Allan, R C. Macknight3 and E Varkonyi-Gasic (2017). Kiwifruit SVP2 gene prevents premature budbreak during dormancy J. Exp. Botany, 68:5, 1071-1082; doi:10.1093/jxb/erx014 -- trinity-only asm :(, evigene reduced K Takishita, Y Takaki, Y Chikaraishi, T Ikuta, G Ozawa, T Yoshida, N Ohkouchi, K Fujikura (2017). Genomic Evidence that Methanotrophic Endosymbionts Likely Provide Deep-Sea Bathymodiolus Mussels with a Sterol Intermediate in Cholesterol Biosynthesis. Genome Biol Evol; 9 (5): 1148-1160. doi: 10.1093/gbe/evx082 -- trinity-only asm :(, excess methods Evangelistella C , A Valentini, R Ludovisi, A Firrincieli, F Fabbrini, S Scalabrin, F Cattonaro, M Morgante, G S Mugnozza, J J. B. Keurentjes and A Harfouche (2017). De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock. Biotechnology for Biofuels 2017 10:138; doi: 10.1186/s13068-017-0828-7 S. Sanders and M. Pfrender. (2017). deNovo assembly and annotation of Ambystoma laterale and Ambystoma jeffersonianum transcriptomes: the first steps toward investigating polyploid salamander expression. Evolution Conference 2017, Portland, OR. Retrieved from http://hdl.handle.net/2022/21599 L. Bu, S. Buddenborg, S. Zhang and E.S. Loker (2017). Comparative Study Of De Novo Transcriptome Assembly Methods And Potential Impacts On Differential Gene Expression, of the freshwater snail Biomphalaria pfeifferi. 92nd Annual Meeting, American Soc. of Parasitologists. San Antonio, Texas, June 2017 http://amsocparasit.org/node/178 Hui Zhang, L R Goertzen, C Yiwu Chen, E Peatman, and J. S McElroy (2017). Constructing Eleusine Transcriptome References for Determination African Finger Millet (Eleusine coracana) Parentage. Talk at Am.Soc. of Agronomy, Crop Science Soc.Am., Soil Science Soc. Am. https://scisoc.confex.com/crops/2017am/webprogram/Paper104706.html Renuka. P, Maganti. S. Madhav, Padmakumari. A. P, Kalyani. M. Barbadikar, Satendra. K. Mangrauthia, Vijaya Sudhakara Rao. K, Soma S. Marla, and Ravindra Babu. V (2017). RNA-seq of Rice Yellow Stem Borer, Scirpophaga incertulas reveals molecular insights during four larval developmental stages. G3: Genes|Genomes|Genetics doi:10.1534/g3.117.043737 -- used Evigene to reduce Triniy-only gene assembly, also used cd-hit, TGICL -- longest-transcript cluster filtering that reduces gene set accuracy Yerramsetty P, EM Agar, WC Yim, JC Cushman and JO Berry (2017). An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. J. Exp. Botany, doi:10.1093/jxb/erx264 Brown, Stuart M., A Heguy, P Zappile, H Chen, A Goradia, Y Wang, Y Hao, N K. Roy, K Vitale, R. C Chambers, Isaac Wirgin (2017). A Dramatic Difference in Global Gene Expression between TCDD-Treated Atlantic Tomcod Larvae from the Resistant Hudson River and a Nearby Sensitive Population. Genome Biology and Evolution, evx159, doi: 10.1093/gbe/evx159 Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E (2017). Evidence for an ancient whole genome duplication in the cycad lineage. PLoS ONE 12(9): e0184454. doi:10.1371/journal.pone.0184454 -- nice example where gene set precision of Evigene aids phylogenetic inferences Arvind Sundaram, Torstein Tengs, Unni Grimholt (2017). Issues with RNA-seq analysis in non-model organisms: A salmonid example. Developmental & Comparative Immunology, 75:38-47 doi:10.1016/j.dci.2017.02.006. Christodoulides, N (2017). Exploring the transcriptomics of polyphagy in plant-eating insects. Thesis, Auburn University https://etd.auburn.edu/bitstream/handle/10415/5892/NC%20Thesis%20FinalCheck.pdf?sequence=2 Buddenborg SK, Bu L, Zhang S-M, Schilkey FD, Mkoji GM, Loker ES (2017). Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species. PLoS Negl Trop Dis 11(10): e0005984. doi:10.1371/journal.pntd.0005984 Stam, R, G A Silva-Arias, T Nosenko, D Scheikl, A C Horger, W Stephan, G Haberer, A Tellier (2017). A small subset of NLR genes drives local adaptation to pathogens in wild tomato. bioRxiv 210559 preprint, 2017 Oct; doi: 10.1101/210559 Cornelis G, M Funk, C Vernochet, F Leal, O A Tarazona, G Meurice, O Heidmann, A Dupressoir, A Miralles, M P Ramirez-Pinilla, and T Heidmann (2017). An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. PNAS ; eprint November 21, 2017, doi:10.1073/pnas.1714590114 Yang T, L Fang, S Sanders, S Jayanthi, G Rajan, R Podicheti, S K Thallapuranam, K Mockaitis and F Medina-Bolivar (2017). Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins J. Biol. Chem. doi: 10.1074/jbc.RA117.000564 Gambino G, AD Molin, P Boccacci, A Minio, W Chitarra, CG Avanzato, P Tononi, I Perrone, S Raimondi, A Schneider, M Pezzotti, F Mannini, I Gribaudo & M Delledonne (2017). Whole-genome sequencing and SNV genotyping of Nebbiolo (Vitis vinifera L.) clones. Scientific Reports 7, A# 17294; doi:10.1038/s41598-017-17405-y da Silva-Junior OB, D Grattapaglia, E Novaes, RG Collevatti (2017). Genome assembly of the Pink Ipe (Handroanthus impetiginosus, Bignoniaceae), a highly-valued ecologically keystone Neotropical timber forest tree. GigaScience, gix125. doi: 10.1093/gigascience/gix125 Schvartzman, MS, Corso M, Fataftah N, Scheepers M, Nouet C, Bosman B, Carnol M, Motte P, Verbruggen N and Hanikenne M (2018). Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri. New Phytol. doi:10.1111/nph.14949 -- trinity-only gene assembly, + evigene reduction Mun Hua Tan, C M Austin, M P Hammer, Y P Lee, L J Croft, H M Gan (2018). Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly. GigaScience, 7:3, doi: 10.1093/gigascience/gix137 Grapputo A, AH Thrimawithana, B Steinwender and RD Newcomb (2018). Differential gene expression in the evolution of sex pheromone communication in New Zealand's endemic leafroller moths of the genera Ctenopseustis and Planotortrix BMC Genomics 19:94 doi: 10.1186/s12864-018-4451-1 Urbarova I , H Patel, S Foret, BO Karlsen, TE Jorgensen, JM Hall-Spencer and SD Johansen (2018). Elucidating the small regulatory RNA repertoire of the sea anemone Anemonia viridis based on whole genome and small RNA sequencing. GBE early. doi: 10.1093/gbe/evy003/4827693 -- evigene tools Alleman A, B Feldmeyer & S Foitzik (2018). Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes. Scientific Reports 8, A# 1951; doi:10.1038/s41598-018-20262-y Massonnet M, A Morales-Cruz, A Minio, R Figueroa-Balderas, DP Lawrence, R Travadon, PE Rolshausen, K Baumgartner, and D Cantu (2018). Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolism gene clusters in the grapevine Esca pathogen Phaeoacremonium minimum. bioRxiv preprint, 23 Jan 2018; doi: 10.1101/252221; Front. Microbiol., 13 August 2018; doi: 10.3389/fmicb.2018.01784 Oostra V, Saastamoinen M, Zwaan, BJ, Wheat CW (2018). Strong phenotypic plasticity limits potential for evolutionary responses to climate change Nature Communications 9, A# 1005; doi: 10.1038/s41467-018-03384-9 and bioRxiv preprint, 2017 Apr; doi:10.1101/126177 Machadoa AM, M Feliciob, E Fonsecab, RR da Fonsecad, L Filipe C. Castroa, (2018). A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias. Data in Brief, doi: 10.1016/j.dib.2018.03.013i Korani W, Y Chu, CC Holbrook, and P Ozias-Akins (2018). Insight into genes regulating post-harvest aflatoxin contamination of tetraploid peanut from transcriptional profiling. Genetics, 209(1): 143-156; doi:10.1534/genetics.118.300478 -- trinity asm only :(, evigene reduced Hoang NV, A Furtado, PP Thirugnanasambandam, FC Botha, RJ Henry (2018). De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts. Heliyon 4 e00583. doi:10.1016/j.heliyon.2018.e00583 Yurchenkoa AA, Katolikova N, Poleve D, Shcherbakovae I, Strelkov P (2018). Transcriptome of the bivalve Limecola balthica L. from Western Pacific: A new resource for studies of European populations. Marine Genomics, Elsevier. doi: 10.1016/j.margen.2018.03.007 Shalev TJ, Yuen MMS, Gesell A, Yuen A, Russell JH, Bohlmann J (2018). An annotated transcriptome of highly inbred Thuja plicata (Cupressaceae) and its utility for gene discovery of terpenoid biosynthesis and conifer defense Tree Genetics & Genomes, doi: 10.1007/s11295-018-1248-y Han, Z., Xiao, S., Li W.,Ye, K., Wang, Z.Y. (2018). The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora). Genes & Genomics. doi: 10.1007/s13258-018-0697-x Chen Q , X Liu, Y Hu, B Sun, Y Hu, X Wang, H Tang, Y Wang (2018). Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus. International Journal of Genomics, 2018:8084032, doi: 10.1155/2018/8084032 Zhang X, K Xia, L Lin, F Zhang, Y Yu, K St. Ange, X Han, E Edsinger, J Sohn and RJ Linhardt (2018). Structural and Functional Components of the Skate Sensory Organ Ampullae of Lorenzini. ACS Chem. Biol. XXXX, XXX; doi: 10.1021/acschembio.8b00335 Ismail NIB, Y Kato, T Matsuura, H Watanabe (2018). Generation of white-eyed Daphnia magna mutants lacking scarlet function. bioRxiv May. 2, 2018; doi: 10.1101/313395. -- uses daphia magna evigene set and eugenes.org genome database Ueno S, Y Nakamura, M Kobayashi, S Terashima, W Ishizuka, K Uchiyama, Y Tsumura, K Yano, and S Goto. (2018). TodoFirGene: developing transcriptome resources for genetic analysis of Abies sachalinensis. Plant Cell Physiol. 0(0):1-9; 15 March 2018; doi:10.1093/pcp/pcy058 Venturini L, S Caim, G G Kaithakottil, D L Mapleson and D Swarbreck. (2018). Leveraging multiple transcriptome assembly methods for improved gene structure annotation. GigaScience, 2018, 0(0):1-13; doi:10.1093/gigascience/giy093/5057872 -- mikado is built upon evidentialgene methods to new chromosome-aligned gene assembly pipeline Gan, H.M., Austin, C. & Linton, S (2018). Transcriptome-Guided Identification of Carbohydrate Active Enzymes (CAZy) from the Christmas Island Red Crab, Gecarcoidea natalis and a Vote for the Inclusion of Transcriptome-Derived Crustacean CAZys in Comparative Studies. Mar Biotechnol. doi: 10.1007/s10126-018-9836-2 Richardson MF, F Sequeira, D Selechnik, M Carneiro, M Vallinoto, JG Reid, AJ West, MR Crossland, R Shine, LA Rollins (2018). Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. GigaScience, 7:1.1, gix114, doi: 10.1093/gigascience/gix114 Zhang, Hui (2018). Expanded Understanding of Eleusine Diversity and Evolution PhD. Dissertation, Auburn, Alabama; http://hdl.handle.net/10415/6253 or doi:10415/6253 Sohrabi, SS, A Ismaili, FN Firouz-Abadi, H Fallahi (2018). Discovery of EST-SSRs Markers in Lentil (Lens culinaris) under Cold Stress. Crop Biotech., Summer (2018) 22: 1-14 (in Persian) Visser, Erik A., Jill L. Wegrzyn, Alexander A. Myburg and Sanushka Naidoo. (2018). Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation). BMC Genomics 19:632; doi: 10.1186/s12864-018-5015-0 Maex M, D Treer, H De Greve, P Proost, I Van Bocxlaer, F Bossuyt (2018). Exaptation as a Mechanism for Functional Reinforcement of an Animal Pheromone System, Current Biology, in press, 2018-Sep; doi: 10.1016/j.cub.2018.06.074 Huerlimann R, NM. Wade, L Gordon, JD. Montenegro, J Goodall, S McWilliam, M Tinning, K Siemering, E Giardina, D Donovan, MJ. Sellars, JA. Cowley, K Condon, GJ. Coman, MS. Khatkar, HW. Raadsma, GE. Maes, KR. Zenger & DR. Jerry (2018). De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Scientific Reports, 8:13553 ; doi: 10.1038/s41598-018-31148-4 Edsinger E. and G Dolen, (2018). A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus. Current Biology, doi: 10.1016/j.cub.2018.07.061 Minio A, M Massonnet, R Figueroa-Balderas, AM. Vondras, B Blanco-Ulate, and D Cantu (2018). Iso-Seq allows genome-independent transcriptome profiling of grape berry development. bioRxiv preprint, 5 Nov 2018; doi: 10.1101/269530 G3: Genes|Genomes|Genetics, 14 Jan 2019; doi:10.1534/g3.118.201008 Vita F, A Alpi, E Bertolini (2018). De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico) bioRxiv preprint, 4 Nov 2018; doi: 10.1101/461483 Hamilton PT., CN. Hodson, CI. Curtis, and SJ. Perlman (2018). Genetics and Genomics of an Unusual Selfish Sex Ratio Distortion in an Insect. Current Biology 28, 1-7 December 3, 2018, doi:10.1016/j.cub.2018.10.035 Hasegawa Y, Ueno S, Matsumoto A, Ujino-Ihara T, Uchiyama K, Totsuka S, et al. (2018). Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don). 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PLoS ONE 18(6): e0287294. doi: 10.1371/journal.pone.0287294 --------------- Alabama Supercomputer Authority Installed Software and Tools includes EvidentialGene https://www.asc.edu/supercomputing/software.shtml Swedish Bioinformatics Support, Biosupport.se Supported biosoftware includes EvidentialGene doi: 10.1186/2047-217X-2-9, PMCID: PMC3704847 Oilseeds Biochemical Genomics project, NSF-Award# 1339385 http://bioinfolab.unl.edu/oilseeds/pipeline.html Purdue University, Bioinformatics Core facility https://wiki.itap.purdue.edu/display/BioCoreFacility/Bioinformatics+software+listing National Center for Genome Analysis Support, https://ncgas.org/ de novo transcriptome assembly pipeline with EvidentialGene Phytozome genome of Anacardium occidentale (Cashew tree), 2018 Cashew gene set reconstruction includes EvidentialGene use https://phytozome.jgi.doe.gov/ EvidentialGene has been developed and used in various other gene/genome projects by the author in collaborations since 2009, some papers are in print. -------------------------------------------------------------------- In_draft: Gilbert, DG. (2019). Longest protein, longest transcript or most expression, for accurate gene reconstruction of transcriptomes? bioRxiv 829184; doi: 10.1101/829184 In_review: Published: Gilbert, DG. 2019. Genes of the Pig, Sus scrofa, reconstructed with EvidentialGene. PeerJ 7:e6374; doi:10.7717/peerj.6374 BioRxiv pre-peer-review, Sep 2018. doi: 10.1101/412130 Pig gene data set, NCBI TSA accession DQIR00000000, and doi 10.5967/K8DZ06G3 at scholarworks.iu.edu archive. Orsini L, Brown JB, Shams Solari O, et al. [includes DGG] 2017. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. Mol Ecol. 2017;00:1-12. doi: 10.1111/mec.14261 Noah M. Reid, Craig E. Jackson, Don Gilbert, Patrick Minx, Michael J. Montague, Thomas H. Hampton, Lily W. Helfrich, Benjamin L. King, Diane E. Nacci, Neel Aluru, Sibel I. Karchner, John K. Colbourne, Mark E. Hahn, Joseph R. Shaw, Marjorie F. Oleksiak, Douglas L. Crawford, Wesley C. Warren, Andrew Whitehead (2017). The Landscape of Extreme Genomic Variation in the Highly Adaptable Atlantic Killifish. Genome Biol Evol 2017; 9 (3): 659-676. doi: 10.1093/gbe/evx023 # EvigeneH hybrid RNA/DNA gene set that NCBI has difficulties accepting, despite their own pipeline # producing similar genes corrected for chromosome-assembly errors . # NCBI Genbank annotated genome submission still "in progress", but submit set is available and passes most checks. Luisa Orsini, Donald Gilbert, Ram Podicheti and others. (2016) Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors, Scientific Data. doi:10.1038/sdata.2016.30 # reports accurate, high quality gene assemblies from EvigeneR (NCBI TSA, GDIP00000000 and GDIQ00000000 of 2 populations), # and a better EvigeneH hybrid RNA/DNA gene set that NCBI won't accept as a hybrid of gene data dogmas. Daphnia magna Genome Consortium (2016). Daphnia magna genome annotated assembly draft v2.4. NCBI/DDBJ/ENA GenBank accession LRGB01000000, BioProject PRJNA298946 # contains the chromosome-modeled genes that contribute to better EvigeneH hybrid RNA/DNA gene set. Alfredo Rago, Donald Gilbert, Jeong-Hyeon Choi, Tim Sackton, Xu Wang, Yogeshwar Kelkar, John H. Werren, John K. Colbourne Genome Re-Annotation of the Jewel Wasp Nasonia vitripennnis BMC Genomics, 2016; 17(1): 678. doi: 10.1186/s12864-016-2886-9; PMCID: PMC5000498 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000498/ # reports on older methods of EvigeneD gene construction (chromosome-DNA-assembly modelled) Motamayor, J. C., Mockaitis, K., Schmutz, J., et al. [includes DGG] (Cacao Genome Group) 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating traits: pod color as an example. Genome Biol. Jun 3;14(6):r53. PMID: 23731509. # an accurate, high quality gene set to go with the high qual chromosome assembly, EvigeneD + early EvigeneR methods. Gulia-Nuss M, Nuss AB, Meyer JM, et al. [includes DGG] Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun. 2016 Feb 9;7:10507. doi: 10.1038/ncomms10507. PMID: 26856261 # as with pine, evigene trasm of tick genes much more ortho-complete than genome-gene models Neale DB, Wegrzyn JL, Stevens KA, et al. [includes DGG] 2014. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol. Mar 20;15(3):R59., PMID: 24647006. doi:10.1186/gb-2014-15-3-r59; # not much dgg work, but evigene gene assembly is reported, and is much more ortho-complete than MAKER genome-gene set # EvidentialGene prelim poster/paper Gilbert, Donald (2010) Perfect(ing) Arthropod Genes with Next Gene Informatics 4th annual Arthropod Genomics Symposium. Kansas State U. http://arthropods.eugenes.org/EvidentialGene/about/PerfectGenes2010.pdf Gene modeling contributions by DGG as precursor to EvidentialGene Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, et al., 2011. The Ecoresponsive genome of Daphnia pulex, Science, 331:555, doi:10.1126/science.1197761 The Nasonia Genome Working Group, 2010. Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species. Science, 327: 343-348; doi: 10.1126/science.1178028; PMID: 20075255. The International Aphid Genomics Consortium, 2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biology, 8(2): e1000313; doi:10.1371/journal.pbio.1000313. Gilbert, D.G., 2007. DroSpeGe: Rapid access Drosophila species genomes database. Nucleic Acids Res. D480-D485 doi:10.1093/nar/gkl997. Clark, AG; Eisen, MB; Smith, DR; Bergman, CM; et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450:203-218. PMID: 17994087 -------- Related software docs that help explain Evigene's success/value: Haznedaroglu et al.: Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. BMC Bioinformatics 2012 13:170. doi:10.1186/1471-2105-13-170 Yu Peng et al.: IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. Bioinformatics, Vol. 29 ISMB/ECCB 2013, pages i326-334 doi:10.1093/bioinformatics/btt219 ---- Comment on Hoang et al, 2017. (above) sugarcane comparison of Pac-Bio RNA versus Illumina RNA * independent comparison of Pac-Bio RNA versus Illumina RNA over-assemblies, with Evigene reduction. I think their assembly methodology for Illumina is overly complex and led to reduced quality of those. In particular they applied too many filters (cd-hit clustering, velvet/oases -merge) which remove valid alternate transcripts, and which can add errors, based on my work with these. Their Methods say "To remove the redundancy, all [CLC/Soap] contigs were pooled and clustered using CD-HIT-EST .. with 95% identity, to obtain one representative assembly. " This will remove valid alternates as they can have >= 95% identity. More important, use of cd-hit-est for longest transcript per cluster selects for errors: indels and joins that lengthen transcripts beyond true size, and break coding sequences. See examples at http://arthropods.eugenes.org/EvidentialGene/evigene/docs/cdhiterr-arabidopsis-example.txt Evigene's pipeline handles over-assemblies to reduce to a most representative coding gene set, based on coding sequence metrics, retaining valid alternates. For Velvet/Oases, use of the option '-merge yes' removes valid transcripts, and creates problem transcripts (false joins). Their table 2 of per assembler results also suggests to me that different options, and less filtering with Velvet/O and Soap would have resulted in much improved assemblies. I always get better results w/ those two than with Trinity. This paper is indicative of the difficult task of determining methods for accurate gene reconstruction. My results with assembly of Illumina vs Pac-Bio are opposite, assembly of Illumina RNA with with different methods yeild more accurate, complete gene sets, including more complete alternate transcripts and paralogs, than the PacBio data I've compared these with for Arabidopsis, corn, and pine trees.