|.... 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 genesGenome size estimates from flow cytometry
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.
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Parent Directory 13-Jun-2023 14:55 - daphnia_genoasm20summary/ 13-Apr-2021 15:44 - daphnia_genomemaps/ 17-Dec-2020 21:07 - dcar20pubasm/ 11-Dec-2020 15:17 - Daphnia carinata publi> dmag20newasm/ 17-Dec-2020 14:22 - Daphnia magna new asse> dmag20pubasm/ 17-Dec-2020 13:37 - Daphnia magna public a> dplx20pubasm/ 17-Dec-2020 20:51 - Daphnia pulex public a> daphnia_gasm20set_info.txt 24-Dec-2020 13:18 5k daphnia_gasm20set_assemblies.txt 15-Dec-2020 14:33 9k daphnia_species_genome_sizes2020.pdf 10-Dec-2020 13:12 9k daphnia_species_genome_sizes2020.png 10-Dec-2020 14:00 191k daphnia5cmp_gdcov7t.chr03anb.pdf 13-Jul-2020 23:06 1.5M