Additional file 1. Assembly characteristics of all assembled crustacean
genomes. Characteristics listed are: species, whether the species genome
is annotated yes or no, N50 of the fragments with the highest assembly
hierarchy, number of fragments with the highest assembly hierarchy in
the assembly, haploid genome size, assembly size, completeness of the
assembly (=haploid GS/assembly size), taxonomic lineage (NCBI
taxonomy), reference for the genome paper.
Additional file 2. Evolution of Artemia assembly quality metrics
throughout the assembly steps. Evolution of the scaffold N50, the
number of fragments and the genome completeness (assembly size/
genome size) in the subsequent Artemia assembly stages
Additional file 3 BUSCO analysis results for the A. franciscana genome
assembly and annotation.
Additional file 4. BLAST results for mitochondrial genes in the Artemia
genome. Listed: Query accession and gene name, presence of a
(significant) BLAST hit in the Artemia proteome with the highest bit score,
E-value and bit score of the hit, scaffold length of the scaffold on which
the hit lies, percentage of mitochondrial genes on this scaffold.
Additional file 5. Taxonomic groups of alien genomes identified in the
Artemia genome.
Additional file 6 Expanded or contracted Artemia orthogroups
compared to other Branchiopoda. Listed: Orthogroup ID, number of genes in this orthogroup in A. franciscana, D. pulex, L. arcticus, and E.
texana, expanded or contracted status of the orthogroup in Artemia
compared to D. pulex, L. arcticus and E. texana, conservation in
Branchiopoda (whether this orthogroup contains genes for each
branchiopod), comma-separated IPR description of Artemia genes in this
orthogroup, Artemia genes in this orthogroup.
Additional file 7 GO enrichment of Artemia compared to other
Branchiopoda. Listed: GO ID, name and category, false discovery rate
(FDR) and P value of the Fisher’s exact test enrichment analysis in
Blast2GO, number of Artemia genes from expanded/contracted
orthogroups in this GO ID, number of whole Artemia genome genes in
this GO category, number of Artemia genes from expanded/contracted
orthogroups in this GO ID without GO annotation. The Fisher’s Exact Test
is sensitive in the direction of the test: the genes that are present in the
test-set and also in the reference genome set will be deleted from the
reference, but not from the test set, resulting in zero sequences in the
reference set and values above zero in the test set. Significantly enriched
GOs (FDR ≤ 0.05, biological process) of Artemia genes in expanded or
contracted orthogroups compared to Branchiopoda are given.
Additional file 8 Expanded or contracted Artemia and H. dujardini
orthogroups compared to other Arthropoda. Listed: Orthogroup ID,
number of genes in this orthogroup in A. franciscana and in the other
arthropod species, expanded or contracted status of the orthogroup in
Artemia compared to the other arthropod species, comma-separated IPR
description of Artemia genes in this orthogroup, H. dujardini genes in this
orthogroup, Artemia genes in this orthogroup.
Additional file 9. STAR mapping statistics for differential expression
analysis in Artemia. Listed: sample name, total number of reads for this
sample, percentage of uniquely mapped reads, absolute number of
uniquely mapped reads, percentage of multi mapped reads, absolute
number of multi mapped reads.
Additional file 10. Summarization statistics for differential expression
analysis in Artemia. Listed: sample name, total counts, percentage of
counts assigned to a gene annotation, absolute counts assigned to a
gene annotation. * notice that this amount can be more than the sum of
uniquely mapped + multi-mapped in the mapping statistics since multimapped
reads are considered.
Additional file 11 Differentially expressed genes under high salinity
(p < 0.05). Listed: functional annotation of the differentially expressed
gene, gene ID in the genome annotation and on the ORCAE platform, p
value, average log fold change of gene expression under high salinity,
gene regulation of the differentially expressed gene (up or down),
InterPro description of the gene family to which the gene belongs.
Additional file 12 Differentially expressed genes under anoxia (p < 0.05).
Listed: functional annotation of the differentially expressed gene, gene ID
in the genome annotation and on the ORCAE platform, p value, log fold
change of gene expression under anoxia, gene regulation of the
differentially expressed gene (up or down), InterPro description of the
gene family to which the gene belongs.
Additional file 13 GO enrichment in Artemia under high salinity.
Significantly Enriched GOs (FDR ≤ 0.05) of Artemia genes differentially
expressed under high salinity. Listed: GO ID, name and category, false
discovery rate (FDR) and P value of the Fisher’s exact test enrichment
analysis in Blast2GO, number of DEG under high salinity in this GO
category, number of whole Artemia genome genes in this GO category,
number of DEG under high salinity without GO annotation. The Fisher’s
Exact Test is sensitive in the direction of the test: the genes that are
present in the test-set and also in the reference genome set will be deleted
from the reference, but not from the test set, resulting in zero sequences
in the reference set and values above zero in the test set.
Additional file 14 Pathway enrichment in Artemia under high salinity.
Significantly enriched (Fisher’s exact test corrected for multiple testing,
FDR ≤ 0.05) pathways of Artemia genes differentially expressed under
high salinity. Listed in first worksheet (STRING annotation): gene number,
ORCAE gene ID, STRING Daphnia pulex gene ID, BLAST identity and bit
score, gene name and gene annotation. Listed in second worksheet
(STRING pathway enrichment): KEGG Daphnia pulex pathway name,
pathway description, number of DEG under high salinity in this pathway, number of genes in the D. pulex genome that belong to this pathway,
enrichment FDR, matching D. pulex gene IDs, matching gene names in
pathways shown in figures and additional files, matching D. pulex gene
ID labels.
Additional file 15. Consolidation of DEG analysis, GO enrichment and
pathway enrichment in Artemia under high salinity.
Additional file 16. The enriched Carbon metabolism pathway in
Artemia under high salinity. Up- and downregulated genes are indicated
on the KEGG map dpx01200.
Additional file 17. GO enrichment in Artemia under anoxia. Significantly
enriched GOs (FDR ≤ 0.05) of Artemia genes differentially expressed under
anoxia. Listed: GO ID, name and category, false discovery rate (FDR) and
P value of the Fisher’s exact test enrichment analysis in Blast2GO, number
of DEG under anoxia in this GO ID, number of whole Artemia genome
genes in this GO ID, number of DEG under anoxia without GO
annotation. The Fisher’s Exact Test is sensitive in the direction of the test:
the genes that are present in the test set and also in the reference
genome set will be deleted from the reference, but not from the test set,
resulting in zero sequences in the reference set and values above zero in
the test set.
Additional file 18 Pathway enrichment in Artemia under anoxia.
Significantly enriched (Fisher’s exact test corrected for multiple testing,
FDR ≤ 0.05) pathways of Artemia genes differentially expressed under
anoxia. Listed in first worksheet (STRING annotation): gene number,
ORCAE gene ID, STRING Daphnia pulex gene ID, BLAST identity and bit
score, gene name and gene annotation. Listed in second worksheet
(STRING pathway enrichment): KEGG Daphnia pulex pathway name,
pathway description, number of DEG under anoxia in this pathway,
number of genes in the D. pulex genome that belong to this pathway,
enrichment FDR, matching D. pulex gene IDs, matching gene names in
pathways shown in figures and additional files, matching D. pulex gene
ID labels.
Additional file 19. Consolidation of DEG analysis, GO enrichment and
pathway enrichment in Artemia under anoxia.
Additional file 20. The enriched N-glycan biosynthesis pathway in Artemia
under anoxia. Up- and downregulated genes are indicated on the
KEGG map dpx00510.
Additional file 21. The enriched Basal transcription factors pathway in
Artemia under anoxia. Up- and downregulated genes are indicated on
the KEGG map dpx03022.
Additional file 22. Augustus custom training files for Artemia. Includes
probabilities, parameters and weights used for Augustus training for
annotation of the Artemia genome.
Additional file 23. EuGene custom parameter file for Artemia. Includes
parameters used for EuGene training for annotation of the Artemia
genome.
Additional file 24. Sequence GC-content profiles for all samples used
for differential expression analysis.
