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Daphnia genome assemblies 2020

Daphnia genome assemblies, 2020 assessment, in-progress results
Don Gilbert, http://wfleabase.org/genome/Daphnia_species_genomes/

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 carinata : 254 Mb (0.26 pg [3]);
Daphnia magna(s) : 234-391 Mb (0.240-0.40 pg [2,3] );     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);   4. doi: 10.1534/g3.119.400560

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.

Daphnia species Genome Sizes

measured with flow cytometry, DNA assembly (observed), and assembly sizes estimated 
with DNA coverage depth at conserved, unique gene spans.  Assemblies are measured for 
unique and duplicated DNA read spans, gene coding sequence DNA spans, transposons, repeats and other. 

Duplicated DNA (multi-map reads) and CDS-DNA (DNA mapping to gene coding sequences)
are separately measured attributes, though spans can be both.  These appear 
to be two attributes that may explain large (near 50%) discrepancies in measures 
of Daphnia genome sizes, as the contribute to many 10s of megabase of these genomes.  
Note their large differences with Fruitfly and Daphnia.  

Daphnia's unusual excess of coding-like spans and duplicate spans affect genome assemblers, 
which have difficulties with non-unique genome regions.  Transposon regions with duplicated 
DNA, along with coding regions, in Daphnia appear as large contributors to the assembly size discrepancies.
See Gnodes/Genome Depth Estimator for animals & plants, with Daphnia results.
     

NOTE 2020-Dec: These are in-progress results.  Use with the caveat these data and details 
are being updated, this snapshot will not be preserved and should not be relied on as vetted results. 

      Name                                 Last modified       Size  Description

[DIR] Parent Directory 17-Dec-2020 21:23 - [   ] daphnia5cmp_gdcov7t.chr03anb.pdf 13-Jul-2020 23:06 1.5M [TXT] daphnia_gasm20set_assemblies.txt 15-Dec-2020 14:33 9k [TXT] daphnia_gasm20set_info.txt 24-Dec-2020 13:18 5k [DIR] daphnia_genoasm20summary/ 13-Apr-2021 15:44 - [DIR] daphnia_genomemaps/ 17-Dec-2020 21:07 - [   ] daphnia_species_genome_sizes2020.pdf 10-Dec-2020 13:12 9k [IMG] daphnia_species_genome_sizes2020.png 10-Dec-2020 14:00 191k [DIR] dcar20pubasm/ 11-Dec-2020 15:17 - Daphnia carinata publi> [DIR] dmag20newasm/ 17-Dec-2020 14:22 - Daphnia magna new asse> [DIR] dmag20pubasm/ 17-Dec-2020 13:37 - Daphnia magna public a> [DIR] dplx20pubasm/ 17-Dec-2020 20:51 - Daphnia pulex public a>


Developed at the Genome Informatics Lab of Indiana University Biology Department