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Index of /EvidentialGene/daphnia/Daphnia_species_genomes

      Name                             Last modified       Size  

[DIR] Parent Directory 14-Jul-2020 22:36 - [DIR] genomemaps/ 13-Jul-2020 19:10 - [TXT] daphnia_gasm20set_info.txt 19-Jul-2020 20:02 14k [   ] daphnia5cmp_gdcov7t.chr03anb.pdf 13-Jul-2020 23:06 1.5M

Daphnia genome assemblies, 2020 assessment
Don Gilbert,

Rough taxa distances (cf. Ebert+ 2019 paper)

     |...... Daphnia magna (Europe & S. Korea)  : 3 chr-assemblies, annotated gene transcripts, 
     |                                              Dmag19sk chr-level is reported for now, others later
 |   |..... Daphnia carinata (Australia)        : 1 chr-assembly, Dcari20 chr-level
 |     |... Daphnia similis (China ?)           : annotated gene transcripts mapped to Dcari20.
 |.......... Daph. pulex (N. America)           : 3 chr-assemblies, annotated gene transcripts

Genome size estimates from flow cytometry
  Daphnia pulex(es) [ref1]: 0.22-0.27 pg, or 215-264 Mb, monoploid genome size
  Daphnia magna(s) [ref2]: 0.24-0.40 pg, 234-391 Mb
  Daphnia carinata [ref2]: 0.26 pg, 254 Mb
  Drosophila pseudoobscura [ref3]: 161-180 Mb (male,female)

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.

Developed at the Genome Informatics Lab of Indiana University Biology Department