# genowork/genes2/evigene_plantanimal_17sum.txt Recent Animal and Plant gene set reconstructions with EvidentialGene: Comparisons to other popular and recent gene reconstructions D.G. Gilbert, gilbertd at indiana.edu, 2016/2017 ------------ Comparison to gene sets of other methods, including Pac-Bio RNA sequencing, Trinity-Illumina assembly, and genome gene models, indicate the Evigene methods are more accurate than commonly used methods. In particular, for 3 plant species sets, Illumina RNA assemblies done according to Evigene methods surpass Pac-Bio RNA genes not only in total gene set accuracy, but in per-locus accuracy, where both methods recover some transcripts, for primary, alternate and paralog transcript reconstruction. Trinity assembled Illumina RNA gene sets are likewise incomplete compared to Evigene's multiple-assembler/reduction approach. In comparison to genome-modeled gene sets, that are derived from many sources of gene evidence (prediction on chromosomes, RNA, other species proteins), Evigene's RNA-only constructions often surpass accuracy of those modeled genes. This is likely due to the greater complexity of merging many evidence sources in modeled genes, with greater chances of mis-modeling. These measures of gene set completeness are based on the two basic gene evidence data of protein homology across species, and recovery of expressed sequence evidence. Evigene Illumina-RNA versus PacBio RNA comparisons include below summarized Arabidopsis model plant, Zea mays corn, and pine trees. Evigene vs Trinity-only comparisons include these plants and animals such as Bemisia whitefly, Daphnia water fleas, Aedes and Anopheles mosquitoes, honey bee, mice, fishes and others (including several by independent authors of animal and plant gene sets). Evigene versus genome modeled sets include those produced by NCBI EGAP and MAKER pipelines, AUGUSTUS and similar gene modelers, for Arabidopsis, corn, pine and other plants, and animals including mosquitos, water fleas, honey bee, and others. Zebrafish model animal is added for 2017-Dec reconstruction with Evigene methods, compared with the modelled gene sets of NCBI and Ensembl, surpassing both on average for complete fish/vertebrate protein homology and intron recovery. This draft evigene zebrafish set contains incomplete genes however, as with arabidopsis, only a small subset of RNA data was used, and selecting that subset to include full expression of all genes is difficult as most studies provide RNA of specific tissues for experimental approaches. ------------------------------------------------- 1. Plant model Arabidopsis thal. gene reconstructions compared Gene assemblies of Illumina RNA-seq vs PacBio AtAraport genes Cacao genes Introns Geneset Found% AlignT% Found% AlignF% Found% AtAraport -- -- 88.7 70.6 88.1 AtEvigene 95.4 95.0 89.8 70.2 87.6 AtOases 90.0 91.2 na na 81.1 AtIDBAtr 89.5 89.1 na na 80.7 AtSOAPtr 88.9 87.0 na na 79.1 AtTrinity 88.4 84.1 na na 81.4 AtPacBio 58.1 48.2 64.2 60.5 56.3 -------------------------------------------------------- 2. Corn Zea mays gene reconstructions compared Gene assemblies of Illumina, PacBio, and genes modeled on chromosome assembly Sorghum genes Introns Geneset Found% AlignT% Found% ZmEvigene 82.9 91.1 68.7 ZmGramene 81.9 90.3 68.1 ZmNCBI 81.3 89.6 na ZmPacBio 78.0 82.4 68.2 ZmJgi4 77.6 81.2 68.9 ------------------------------------ 3. Whitefly Bemisia tabaci gene reconstructions compared Reference species RNA Pea aphid Fruit fly Introns Geneset Found% AlnT% Found% AlnT% Found% BtEvigene 81.2 88.0 74.1 74.9 68.5 BtNCBI 79.7 82.3 73.4 71.6 69.4 BtMaker 77.4 73.8 72.1 66.0 57.7 BtTrinity 73.5 59.2 68.0 53.2 50.5 ---------------------------------------------- 4. Water flea Daphnia pulex gene reconstructions compared Reference species RNA Daphnia magna Fruit fly Introns Geneset Found% AlnT% Found% AlnT% Found% DpEvigene 72.0 88.6 67.9 80.3 66.6 DpMaker 58.9 69.9 64.3 74.5 46.7 ---------------------------------------------- 5. Zebrafish model Danio rerio gene reconstructions ... zebrafish17evigene Evigene RNA assemblies vs NCBI, Ensembl genome-gene models Cavefish Human genes Vertebrate_BUSCO Introns Geneset Found% AlnT% Frag% Found% AlnT% Frag% Align Miss Frag Found% DrEvigene 97.0 96.5 0.5 87.5 90.8 0.5 446.8 9 5 81.6 DrNCBI 93.9 92.7 3.9 86.9 89.3 1.2 434.6 19 13 76.4 DrEnsembl 93.1 90.3 5.7 86.3 88.4 2.2 428.2 29 47 57.6 ------------------------------ ------------------ ----------------- ----- Arabidopsis gene set versions AtAraport = public gene set of 2016 of Arabidopsis thal. from Araport.org AtEvigene= Evigene classification/reduction of Illumina RNA assemblies http://arthropods.eugenes.org/EvidentialGene/plants/arabidopsis/evigene2017_arabidopsis/ AtOases = Velvet/oases assembly of Illumina RNA, AtIDBAtr = idba_tran asm of Ill. RNA, AtSOAPtr = SOAP-Trans asm of Ill. RNA, AtTrinity = Trinity asm of Ill. RNA, AtPacBio = Pac-Bio "no-assembly" assembly (PacBio xxx method) of Pac-Bio RNA data Corn gene sets ZmEvig = Evigene Zeamay5fEVm 2016 assembly of Illumina RNA-seq, public at http://arthropods.eugenes.org/EvidentialGene/plants/corn/evg5corn/ ZmGram = Ensembl/Gramene 2016.09 Zm000nnnn, ZmPacb = CSHL/Gramene PacBio gene assemblies of 2016 as SRA entries SRR3147024..054, ZmNCBI = NCBI 2014 refgen zeamay ZmJgi4 = JGI Rnnotator assembly set of Illumina RNA-Seq , 2014 Bemisia tabaci gene sets compared BtEvig = Evigene gene assembly, 2016 update (vers 3), available [soon] at http://arthropods.eugenes.org/EvidentialGene/arthropods/whitefly/whitefly3evigene/ BtNCBI = NCBI RefSeq gene models, 2016 BtMakr = Whitefly genome project genes modeled with MAKER, 2016, whiteflygenomics.org BtTrin = TSA.GBII gene assembly 2015, Trinity of Illumina Daphnia pulex gene sets DpEvig7 Evigene genes of 2017 from http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_pulex/daphnia_pulex_genes2017/ DpMaker7 genes of 2017 from report of doi:10.1534/g3.116.038638 Danio rerio gene sets DrEvigene = Evigene gene assembly, 2017 Dec http://eugenes.org/EvidentialGene/vertebrates/zebrafish/zebrafish17evigene/ DrNCBI = NCBI RefSeq gene models, 2016 Dec, accession GCF_000002035.5_GRCz10 DrEnsEMBL = Ensembl gene models, 2017 Nov Measures Genes Found% = percent of reference genes with significant alignment to gene sets (BLASTp/n of proteins or CDS), Genes AlnT% = percent of aligned bases of reference gene bases Introns Found% = percent of evidence introns aligned to gene set exons, intron evidence from Illumina RNA-seq mapped to chromosome assemblies Further details are in evigene_plantsanimals_2017.txt