Daphnia genome assemblies, 2020 assessment, in-progress results
by Don Gilbert, http://wfleabase.org/genome/Daphnia_species_genomes/
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Rough taxa distances (cf. Ebert+ 2019 paper)

     |.... Daphnia magna (Europe)      : 3+ chr-assemblies, annotated genes 
 ----|
  |  |.... Daphnia carinata (Australia) : 1 chr-assembly 
  |    |.. Daphnia similoides (China ?) : annotated genes mapped to D.cari
  |
  |........ Daphnia pulex (N. America)   : 3 chr-assemblies, annotated genes

Genome size estimates from flow cytometry
  Daphnia pulex(es) : 190-264 Mb (0.193-0.25 pg [1,2] )
  Daphnia magna(s)  : 234-391 Mb (0.240-0.40 pg [2,3] )
  Daphnia carinata  : 254 Mb (0.26 pg [3])
  Drosophila pseudoobscura : 161-180 Mb (male-female [4])
  Refs: 1. doi: 10.1111/j.1095-8312.2008.01185.x (2009); 2. doi: 10.1186/1471-2164-15-1033 (2014); 
     3. http://www.genomesize.com/ (Daphnia refs there); 4. doi: 10.1534/g3.119.400560

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Genome-wide excess DNA depth discrepancies on Dcari20 and Dmagna19 assemblies, somewhat on
Dpulex16, suggest these assemblies are missing a large amount of duplicate-gene,
and transposon, sequence. Estimated missing assembly from DNA depth gives values near
to the Flow cytometry estimated genome sizes.


Table DC1b. Excess DNA coverage depths (XC) measured for Daphnia genome assemblies,
observed and estimated genome sizes, and portion with coding sequences (CDS)
and duplicated regions (Dup), including transposons.
-------------------------------------------------------------------- 
   Assembly  CDS  Dup XC  ObsMb EstMb FlowCy
  -------------------------------------------
    Fruitfly
  Dropse20    33  34  1.0   160  166  160-180 Mb
    Dapnia magna
  Dmagna10    54  22  1.9   134  214  230+ Mb
  Dmagna14    78  79  1.4   180  227  230
  Dmagna19    59  27  1.7   123  192  230
  Dmagna20    86  88  1.0   247  237  230
    Daphnia pulex  
  Dpulex06    60  45  1.0   220  218  200+ Mb
  Dpulex16    60  37  1.1   156  170  200
  Dpulex19    80  89  1.0   190  180  200
    Daphnia carinata
  Dcari20     59  34  1.3   132  162  250 Mb    
  ---------------------------------------------
  CDS = Observed megabases with CDS-mapped reads.
  Dup = Observed megabases of multi-mapped reads.
  XC = XCopy, measure of excess read depth relative to depth at conserved unique genes
  ObsMb = Observed assembly size
  EstMB = Estimated assembly from observed and XCopy excess read depth
  FlowCy = Flow cytometry measured size
  Dropse20, Drosophila pseudoobscura is a control case, from 2020 PacBio-Canu 
   assembly (like dcari20).  

  The ratio of multi-mapping gDNA reads to unique is much higher in 
    Daphnia (55%-66% Dmagna, 52% Dpulex) than Drosophila pse. (23%)
  Dpse CDS cover of 33 Mb is < 1/2 of Daphnia, that appears to be a 
     true, important value based on using same methods.  Daphnia have 
     much more coding sequence than Drosophila, for similar sized genomes.
  These measures are made on 1Kb spans, averaged over a sliding window of 1Kb,
     from samples made at 100 base intervals. The values are an average coverage/1kb 
     of CDS, transposons, repeats, and gDNA reads at a given depth. 
  ========================================================


Duplicate (paralog) gene coding sequence, and transposons are signif. positively
correlated with gDNA read depth.  CDS of unique ortholog genes, and simple
repeats are negatively correlated (ie most at 1x depth, few at higher depth).

Table DC2a.  Correlation of evidence measures with DNA depth on Daphnia assemblies.
DNA depth is relative to 1 for unique gene CDS depth. cdsuni is unique genes CDS spans, 
cdsdup is duplicate/paralog genes CDS spans, repeats are simple repeats and low complexity 
sequence, transposons are RepeatMasker transposon results.

             cdsuni  cdsdup repeats transposons 
  -------------------------------------------
  Dpulex19   -0.089  0.074  -0.093     0.103   
  Dmagna19   -0.351  0.136  -0.111     0.349   
  Dcari20    -0.255  0.263  -0.040     0.285   
  -------------------------------------------


Table DC3c.  gDNA missing from chr assembly but found in gene coding sequences.  
gDNA reads were mapped to both chr-assembly and gene coding sequence.  The proportion 
of reads found in coding sequence missing from chr-assembly is listed.  Miss rates 
below 1% are the expected result; rates above ~1% of same-sample read sets indicate
incomplete assembly at coding sequence loci.

  Species_Asm  CDS_miss 
  -------------------------
    Daphnia magna
  Dmagna10nwb   0.17%   
  Dmagna14bgi   0.12%   
  Dmagna19sk    4.41%   
  Dmagna20skma  0.002%  
  Dmagna20ugma  1.04%   
    Daphnia pulex
  Dpulex16ml    0.6% 
  Dpulex19ml    1.3% 
    Daphnia carinata  
  Dcari20cn     0.2%   
    Drosophila pseudoobscura
  Dropse20      0.0000003% (1 in 3 million)
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