Accurate genes in genome projects: values and problems learned from EvidentialGene
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1 arthropods.eugenes.org/evidentialgene/about/evigenegmod1606iu.pdf Accurate genes in genome projects: values and problems learned from EvidentialGene eugenes.org/evidentialgene/ Don Gilbert 2016 June
2 What is EvidentialGene? Classifier of gene models Class = good, alternate, bad, redundant, coding, non-coding Recipe for gene set reconstruction Over-Assemble genes, from RNA-seq or/and gene predictions Use Coding-Sequence Ruler to select locus representatives Score Homolog alignments to many reference proteins Clean up and publish, via NCBI TSA, other routes Variants EvigeneD = genes modeled on chromosome DNA sequences, EvigeneR = genes assembled from RNA sequences, EvigeneH = hybrid methods of gene reconstruction (in development)
3 Why is Evigene Useful? accurate, objective, simple gene set reconstruction Human protein-coding genome regions are unreliable for 20% of disease genes [1] GMO with inaccurate genes can be a problem, eg. GMO Aedes mosquito [2] Orthology measures are strongly affected by gene inaccuracies [3] (express functions also) Over-assembly is better than one assembly Each locus has own expression values, alternates, neighbor genes that affect assembly Weaknesses of one method compensated by others Gene assembly is better than genome-gene prediction Transposons and long introns are major problems for genome-gene modeling Chromosome assembly gaps, splits, mis-assemblies are common Predictors make poor guesses, even with clean data, un-clean data are common, species training is needed Complex loci, trans-splicing, odd structures on genome are poorly handled, but removed biologically from transcripts. Mosquito examples of Evigene vs MAKER & Trinity of publs [5,6]
4 Ortholog Accuracy in Animals & Plants EvidentialGene reconstructions have more complete alignment to reference genes, versus MAKER, Trinity, NCBI EGAP and other methods, for plants, fish, arthropods. Evigene also builds more complete alternates and non-ortholog sets, but without objective ruler those can be questioned.
5 Evigene: Aedes aegypti GMO region US.FDA, 2016, Oxitec Mosquito: GMO Aedes aegypti OX513A Sect "The combined flanking sequence was compared with the relatively poorly annotated Ae.aegypti genome sequence, transcript and EST databases. The flanking sequence shows 94.6% identity.. to a single genome sequence contig (1.859). No new open reading frames were found.. inferring that no genes appear to be disrupted by the #OX513 rdna construct insertion and no new genes are created.
6 Evigene Compared to... Related gene assembly methods Velvet/O Merge, CAP/extra-assembly,.. don t help much, add errors Other Gene Annotation pipelines with RNA assembly.. see best ortho charts Rnnotator of JGI: similar Over-assembly, Reduce redundancy, NO Coding Ruler, fewer gene classing metrics No-assembly required Single molecule, long read PacBio.. better? is future here?.. very few publ Corn Genes Test Case PacBio long no-assembly + Gramene, Wang et al. (Doreen Ware lab) 2016, doi: / ncomms11708 vs Illumina-short over-assembly, JGI w/ Rnnotator, Martin et al. 2014, doi:0.1038/ srep04519 vs Evigene with Illumina-short over-assembly (same RNA), D. Gilbert, in progress
7 How best to use Evigene with genome projects? Less expertise needed for reliably accurate genes EvigeneR recipe requires less expertise in set up, training, than gene modeling. Accuracy does not depend on quality of chromosome assembly, gene predictor training, nor availability of accurate reference species genes. It does depend on accurate and complete transcribed gene RNA data, but not as much as some think. I recover all but 1% to 5% orthologs, some as fragments, depending on data. Organismal expression from many tissues, stages, stresses, sequenced with current Illumina paired-end, preferably strand-specific, at amounts of Mil pairs/sample. Billions paired reads for more complete genes (rare alternates turn up w/ more data). Gene assembly before chromosome assembly validate gene assembly with reference orthology, then validate/correct chromosome assembly with gene assembly
8 Genome Annotation Workflow, Olive tree 2016-June, lab of Toni Gabaldon, doi: / s
9 Evigene suggested Gene Annotation Workflow, Olive tree
10 What changes to genome projects do Evigene results suggest? Changes to genome projects to add gene assemblies that don t always match chromosome assembly: Match, compare, and merge gene assembly with genome-predicted gene models. Trivial for many loci, hard for some. Add more gene-focused results (annotated transcripts, gene tables) Semi-independence of gene and chromosome data Store outside of GFF/location-based data. Add unlocated transcript-sequence as pseudo-genome scaffolds Alternate transcripts are more plentiful (in biology and gene assemblies). These need analyses (primary/alternate is artificial class), can t be ignored.
11 How does Evigene fit into genome projects? How to assess gene set accuracy and completeness? Ortholog subsets CEGMA, BUSCO, and full assessment with OrthoMCL Expression analyses (read recovery, differential expression,..) Genes reconstructed from transcribed RNA avoid many problems of genomestructure: introns, transposons, alternate exons, trans-splicing, anti-sense splicing are DNA-gene problems. Low expression is an transcribed-gene problem, and assemblers do put wrong pieces together (Evigene removes many). Exceptions in Gene biology and Construction artifacts often look the same.. partial duplications/fragment models, fusions/gene-joins Alternate transcripts are important, under-reported; alternate or paralog of locus?
12 What of many Non-ortholog genes? What to do with Non-ortholog genes? "too many genes? Many throw these away, without positive reason population/related coding conservation (killifish example), differential expression analyses find non-ortho response long non-coding and maybe-coding genes (no coding conservation)
13 Problems of hybrid gene-sets Hybrid gene-set where genes are more accurate than chromosomes (or disagree in places). a. Don't fit dogma nor existing public databases b. Discrepancies can be hard to resolve c. genes!= genome locations -- failed GFF, gn locations to describe genes -- minimal update: always publish gene transcripts (& proteins, cds) sequences. Semi-independent annotation.
14 End note Collaborators and Data Providers Cyber-infrastructure: TeraGrid/XSEDE, NCGAS Genome projects: Cacao Tree, Daphnia Water fleas, Fundulus Fish, Loblolly Pine, Nasonia Wasp, Pea Aphid, and NCBI SRA public data sets References 1. Goldfeder et al., Accuracy in human genome. Genome Medicine, doi: /s GMO Aedes GeneticEngineering/GeneticallyEngineeredAnimals/ucm htm 3. Trachana et al Orthology prediction methods. Bioessays 33: Neafsy et al 2015, Anopheles species genomes. doi: /science Matthews et al. 2016, Aedes aegypti geneset reconstruction doi: /s This Project eugenes.org/evidentialgene/ or sourceforge.net/projects/evidentialgene/
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16 Example Mosquito Gene Accuracy 25 well-conserved Mediator subunit genes of RNA polymerase II transcription, ranging from 2800 aa to 120 aa in size. Evigene reconstructions are compared to 2016 public sets of VectorBase using MAKER (Anopheles) and independent using Trinity (Aedes). Evigene improvements in percent alignment are shown, above zero means improvement, tall bars mean other gene set missed it. Alignment is to Drosophila reference genes.
17 Evigene correction: Fragment (Anoph) & Miss (Aedes) of Mediator subunit gene. Anopheles fun. Evigene vs VB- Maker Aedes aegypti
18 Evigene correction: Join of Small Gene Anopheles fun.
19 Evigene correction: Join of Large Gene Anopheles funestes
20 Coding Sequence Ruler Protein sizes correlate well with homology, across gene sets of a species" Coding sequences discriminate paralogs with same protein Simple to calculate, a coarse ruler for overassembly set Homology (BLASTp) is fine ruler for reduced set
21 Assembly Results for Mosquito Genes Method and KMER effects on best assembly of Highly Conserved Genes of Anopheles funestes Velvet/Oases, , Trinity, , idba-tran, , SOAP-Tr, ,
22 How does Evigene work? (EvigeneR) Over-assemble RNA (100 assemblies/10 M transcripts from 200 M to 10 Bln accurate Illumina paired reads, with de-novo & chr-align methods, several data slices, kmer sizes, options) Find coding sequences (smart ORF/CDS finder) Remove redundancy (stepwise efficient: fastanrdb > cdhit) Classify gene loci (BLASTn, align exons, classify by overlap) Assess orthology (BLASTp reference genes, OrthoMCL) Annotate public sequence products NCBI submission processing
23 Details on how EvigeneR works Algorithm of gene classifier, tr2aacds.pl 1. input transcripts, calculate CDS and AA sequences, work mostly on CDS. 2. perfect redundant removal with fastanrdb (fast) 3. perfect fragment removal with cd-hit-est 4. high-identity align of transcript exons with blastn, to match alternates of each locus. 5. classify main, alternate, redundant transcripts / locus with CDS-align, protein metrics. 6. output classified sequence sets: okay-main, okay-alts, drop (redundant). Other components of gene assembly rnaseq/trformat.pl : regularize and unique IDs for transcript.fasta. omcl/orthomcl_evg.pl, orthomcl_tabulate.pl: protein orthology with BLASTp & OrthoMCL prot/namegenes.pl : gene function names from UniProt and Conserved Domains (CDD). rnaseq/asmrna_trimvec.pl : vector, gap and contaminant screening (suited for NCBI). evgmrna2tsa.pl : check and annotate mrna, public IDs and sequence files, write Genbank TSA format for public submission.
24 Challenge to Galaxy Jockeys Install & test drive Evigene in Galaxy Others use it now at compute centers and in projects, without my help. Evigene needs work on ease of use by non-computists (also computists). One button recipe or script for automated gene assembly is possible, can better link components. Compare to other gene reconstruction method(s) ~3 days/mosquito to build over-assembly and best genes, but weeks to assess & explain their value to others. I will help and collect Galaxy-ready scripts for Evigene more details
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