EvidentialGene: Orthology completeness of Arthropod gene assemblies

2014-Nov, D. Gilbert, gilbertd at indiana edu
2015-Mar update; See also EvidentialGene: Alignment scores of Gene sets Constructed from mRNA-Seq Assembly or Genome Predictions/mappings , 2013

• Orthology completeness of gene sets per Arthropod species-clade
• Conserved Domain gene set completeness for Arthropods, Fishes and Plants
• Orthology completeness across Arthropod species
• Orthology analysis methods
• Honey bee gene sets, per gene alignments
• Daphnia gene sets, per gene alignments
• Tick species gene sets, per gene alignments
• Beetle species gene sets, per gene alignments
• Fruitfly gene sets, per gene alignments

mRNA-assembled genes are constructed without any reference protein information, nor with genome data. Genome gene sets use both reference genes and genomes to produce gene models. I.e., the genome genes have the answers in front of them, while mRNAseq genes do not. Some of these gene set comparisons use the same RNA-seq data, where the genome-based versions have added sources of information, and of errors. If genes can be fully constructed from mRNA-seq alone, then adding genome data, prediction software, and related species proteins may contribute more mistakes than improvements.

This summary shows that Arthropod species gene sets constructed from mRNA-seq are often more complete than genes from genome-modelling methods. mRNA-seq genes are more biologically convincing as they don't rely on the reference species genes, predictions or genome assembly, and thus are not subject to artifacts from those sources. When they match the reference genes, it is true discovery.

Fig 4a. Honey bee	Fig 4b. Daphnia water fleas (D. magna, pulex)	Fig 4c. Ticks (Deer tick, Zebra tick, Spider mite)
Fig 4d. Tribolium Beetle	Fig 4f. Fruit fly	Fig 4. Legend Nref_common = Reference ortholog families found, as percent of common ortholog gene families found in gene set (common set = 8723 groups, common to each of 10 species including these) AaSize = protein size, as percent of ortholog reference protein size Align_common = Alignment to Reference ortholog protein, as percent of ref protein. Best_of_Species = gene set score for all reference orthologs, as percent of all ref gene families, from best, or same as best (tie), align score per reference gene over gene sets. I.e. 100% best for setA = all orthologs have best/tie score for setA, none better in sets B or C, 90% for setA implies 10% better in other gene setB, setC,.. Species gene sets left-right order, newest to oldest, as listed below. Evigene sets are solid color bars, others are hashed color.

Fig 5. Conserved Domain gene-set completeness of Arthropods, Fish and Plants

Fig 5a. Conserved Domains in Arthropod gene sets
Fig 5b. Conserved Domains in Fishes	Fig 5c. Conserved Domains in Plants	Fig 5. Legend Conserved Domains from NCBI CDD (2014.10), subsets by taxonomic group, CD found (a) in Arthropods, (b) in Vertebrates, and (c) in Plants with deltablastp. CD set for Arthropods (a) is determined as Eukaryote CD that occur in all 3 clades Insecta, Crustacea and Chelicerata, in at least one species gene set. pHit = Conserved Domains found, as percent of all conserved domains in species/clade set Alignment = percent Alignment to Domains. Best_of_Species = gene set best with longest alignment, or same as best (tie), per domain, as percent of all domains. I.e. 100% best for setA = all genes have best/tie domain alignment for setA, none better in sets B or C, 60% for setA implies 40% better in other gene sets. Calculations are within species/clade (color coded sets), normalized to 100% of all CD per clade. Arthropod gene sets are left-right ordered, newest to oldest, as listed above. Evigene sets are solid color bars, others are hashed color. Gene set rank order for Best_of_Species are same for Orthology group and Conserved Domain analyses.

             Common Families     All Families
Species   cBits aaSize oMiss tBits oGroup Tiny
--------- ------------------ -----------------
daphniam   650   46     18    466  11523  1.8%
daphniap   643  -25     36    462  11670  5.1%
beetlet    526  -26     42    351   8765  4.1%
beetlep    541   15     78    358   8875  3.5%
honeybee   532   38    161    346   8682  3.1%
fruitfly   470   68    203    290   7801  1.8%
----------------------------------------------

              Common     All Families  
Geneset    cBits aaSize tBits oGroup Tiny
----------------------- -----------------
cacao1evg    653   15    547  15161  0.7%
cacao1cr     641   11    530  14897  1.5%
banana1g     522   -19   371  12537  4.6%
banana1evg   521   -21   349  11733  7.5%
-----------------------------------------

             Common Families    All Families
Species   cBits aaSize oMiss  tBits  oGroup Tiny
--------- ------------------- -------------------
killifish  803     50     18   585   17272   1.1%
maylandia  824     45     76   596   16469   1.1% 
tilapia    822      6    223   568   14905   1.9% 
platyfish  783    -12    118   549   15305   4.7% 
zebrafish  711     -9    366   478   15190   4.8% 
catfish    725     21    729   470   14276   3.4% 
-------------------------------------------------

Orthology analysis methods

2015-Mar update to 2014-Nov assessment

Prior data and plots of 2014-Nov assessment are available here.

Orthology completeness assessment

• Orthology gene groups are those of ARP7 OrthoMCL analysis set of 10 species, group IDs of ARP7f_Gnnn, such as ARP7f_G1000.
  This gene orthology database ARP7 is at arthropods.eugenes.org/arthropods/orthologs/ARP7/,
  including orthology tabulations and annotations, and species gene set proteins.
  Gene family report pages are found with ARP7 IDs at http://arthropods.eugenes.org/genepage/arp7xml/ARP7f_G1000

• Orthology gene groups that are common to all 10 species are used, though missing from some species gene sets, n=8723 listed in allspp-refarp7s10fset1.comgrpid2
  Tables for this analysis were produces using blastp of all transcript proteins (primary and alternate) to the ARP7 OrthoMCL reference protein database (n=131876 proteins of 10 species). The best aligned or best bitscore match of query gene set to reference database is tabulated, along with reference ARP7 gene group. These tabulations exclude same-species matches (query-ref). Alignment score is prefered over bitscore (or e-value) in this analysis because the bitscore is very strongly affected by taxonomic distance, alignment less so. Using bitscore gives different results per gene, but returns the same basic results in overall gene set qualities.

• Tabulation of closest alignment of query genes x reference orthology gene group includes classification of Best_of_Species across gene sets per species, as Best=higher alignment than any others, Same=tied for top alignment (within 2% of top), Diff=lower than top alignment, Miss=no alignment to reference orthology group gene. For Ticks gene sets, related species were grouped into Best_of_Species classification.

• Alignment score tables used for above summaries are in this format

  tgeneset     orgroupid    refgeneid                 trgeneid                    bits    iden    algn    pal     dlen    rsize   tsize   isbest  comorgrp
  amelevg14    ARP7f_G1370  nasvit:Nasvi2EG037131t1   amevg14:Apimel3EVm000005t4  14052   6667    8474    89.9    93.6    9421    8815    best    1
  apimel14nc   ARP7f_G1370  nasvit:Nasvi2EG037131t1   apimel14nc:XP_006568818     12637   6007    7574    80.4    81.2    9421    7654    diff    1
  apismel45    ARP7f_G1370  nasvit:Nasvi2EG037131t1   apismel45:GB55483-PA        13980   6618    8456    89.8    100     9421    9504    diff    1
  apimel1      ARP7f_G1370  nasvit:Nasvi2EG037131t1   apimel1:GB11358-PA          12598   5976    7655    81.3    98.6    9421    9290    diff    1
  
  amelevg14    ARP7f_G251   tribcas:XP_008191512      amevg14:Apimel3EVm000003t2  11260   5507    8819    34.6    40.7    25481   10366   diff    1
  apimel14nc   ARP7f_G251   tribcas:XP_008191512      apimel14nc:XP_006564376     13101   6650    11658   45.8    78.3    25481   19952   best    1
  apismel45    ARP7f_G251   tribcas:XP_008191512      apismel45:GB47977-PA        10029   5206    10376   40.7    91.9    25481   23421   diff    1
  apimel1      ARP7f_G251   tribcas:XP_008191512      apimel1:GB14642-PA          8242    4124    7786    30.6    67.7    25481   17256   diff    1
  

  found here: apismel4set, tribolium4set, daphmag2set, daphplx3set, dromel3set, tick4set
  Alignment score summary table for all species gene sets
  

• ARP7 OrthoMCL analysis includes 10 species, 8 arthropods plus Human and a Fish (maylandia), with species proteins excluding Daph magna available at EvidentialGene/daphnia/daphnia_magna_new/Proteins/
  arp7s10b14nodmag.species.txt

  45212 daphplx Daphnia pulex water flea, 2010 beta gene set (~10,000 noncoding included)
  29127 daphmag Daphnia magna water flea, 2014 gene set
  13927 dromel  Drosophila melanogaster fruit fly, FBgn version 5.x (date?)
  72392 honbee  Apis melifera honey bee, 2014 evigene mRNA-assembly (url)
  39357 human   Homo sapiens human, UniProt 2014 ?
  23194 mayzebr Malandia zeb.. cichlid fish, 2014 NCBI gene set
  36390 nasvit  Nasonia vitripennis jewel wasp, 2010 evigene
  26962 penmon  Pen. mon. tiger shrimp, 2013 evigene mRNA assembly (url)
  21503 pogcha  Pog. cha. beetle, 2013 evigene mRNA assembly (url)
  12420 tribcas Tribolium castenaeum beetle, 2014 NCBI gene set

• OrthoMCL (www.orthomcl.org) methods include reciprocal best blast hit (bbh) of all primary transcript proteins (one protein/gene locus), then tabulation of best reciprocal hits for within (paralog) and between (ortholog) species, followed by Markov clustering (MCL) to form gene groups. Several papers attest to the validity of OrthoMCL and MCL clustering for identifying orthology gene families.

• Conserved Domain analysis is performed with NCBI deltablast, using cdd_delta database of 2014 Oct. CD subsets are derived from taxonomic division common to all sequences provided as representatives of each CD. Longest alignment to each CD, or highest identity, per gene set is used to measure gene set presence (Hit) and score. Alignment and Identity scores give equivalent rank orders for gene sets. Bitscore and e-value are not used because they are confounded by sizes of proteins that are always longer than domains they contain.

• Conserved Domain alignment score tables used for above summaries are in this format

  CDid      CDlen Bestset    Geneset1                      Bit1 Id1 Aln1 Geneset2          Bit2 Id2 Aln2 Geneset3...
  CDD:100015  434 amelevg14  amelevg14:Apimel3aEVm009774t2  928 404 466 apimel1:GB10009-PA  965 395 434 apimel14nc:XP_006558759 896 356 434 ..
  CDD:100016  425 apimel14nc amelevg14:Apimel3aEVm006739t16 942 417 452 apimel1:GB11920-PA  944 391 431 apimel14nc:XP_006567220 663 294 466 ..
  CDD:100017  431 same4      amelevg14:Apimel3aEVm010780t1  880 353 432 apimel1:GB18755-PA  889 353 432 apimel14nc:XP_394981    889 353 432 ..
  

  found here: apismel4set, beetle3eu2e, daphnia2set, dromel3set, tick4set, nasonia3set, plants3set, fish7set (longest alignments),
  with summary tables cdd-alleuks-dompair5sum.txt (longest align) and cdd-alleuks-dompair4sum.txt (highest identity) of the 34 animal and plant species gene sets analyzed.
  Statistics pHit, paln, pbest, the percentages of present (hit), aligned and best score per CD of nRef CD are plotted above, from columns "nRef nHit pHit bits iden algn paln ptop best same diff miss pbest"
  for NCBI CD descriptions and taxonomy in cdd-delta14desc.txt
  

Fig 6a. Honey bee gene sets, per gene alignment to orthology reference genes

Apis Evigene-M 2014, apisevg14 Apis NCBI 2014, apis14nc Apis OGS 4.5, apis45 Apis OGS 1, apis1

Longest orthogene groups (1-200)

Mid sized orthogene groups (1000-1200)

Shorter orthogene groups (5000-5200)

Fig 6b. Daphnia water flea gene sets, per gene alignment to orthology reference genes

Daph. magna Evigene-M 2014, dapmagevg14 Daphnia pulex 2010 Evigene-G, dapplx10evg Daph. magna Evigene-G 2011, dapmag11 Daphnia pulex OGS1, dapplxjgiv11

Longest orthogene groups (1-200)

Mid sized orthogene groups (1000-1200)

Shorter orthogene groups (5000-5200)

Fig 6c. Tick species gene sets, per gene alignment to orthology reference genes

Deer tick Evigene-M 2014, tickixevg14 Deer tick OGS1 2010, tickix Spider mite OGS1, tickte Zebra tick Evigene-M 2013, tickzbevg13

Longest orthogene groups (1-200)

Mid sized orthogene groups (1000-1200)

Shorter orthogene groups (5000-5200)

Fig 6d. Tribolium beetle gene sets, per gene alignment to orthology reference genes

Tribolium Evigene-M 2014, tribcas4evg2 Tribolium AUGUSTUS 2014, tribcas4aug Tribolium NCBI 2014, tribcas14nc Tribolium OGS1, tribcas1

Longest orthogene groups (1-200)

Mid sized orthogene groups (1000-1200)

Shorter orthogene groups (5000-5200)

Fig 6f. Fruitfly gene sets, per gene alignment to orthology reference genes

Fruitfly rel5.48, drosmel548n Fruitfly rel5.0, drosmelr5 Fruitfly rel4, drosmelr4

Longest orthogene groups (1-200)

Mid sized orthogene groups (1000-1200)

Shorter orthogene groups (5000-5200)