Genome Browser

The genome browser is searchable using a Hydractinia scaffold or gene identifier as the query. Note that scaffold names take the form HySX for H. symbiolongicarpus or HyEX for H. echinata, where “X" is a padded four digit numbers (e.g., HyS0001, HyS0010, HyS0100, HyE0002, HyE0200). Gene identifiers take the form “HySX.N” or "HyEX.N", where "N" is a non-padded number (e.g., HyS0459.4, HyE0001.10).

          


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H. symbiolongicarpus

H. echinata                          

Tracks available on the Hydractinia Genome Browser:

Track	Description	H. symbiolongicarpus	H. echinata
Aligned RNA-seq: DevTimeSeries * (e.g., 4c1, 16c1, 64c1, 24h1, etc.); BL* and PB* (e.g., BL1C, PB1C, etc.)	RNA-seq reads from a H. symbiolongicarpus developmental time series with four stages (4 cell, 16 cell, 64 cell, and 24 hours) and a H. echinata polyp head regeneration experiment with two time points (presumptive blastema, PB, at 0h and blastema, BL, at 24h post head removal) were aligned to the H. symbiolongicarpus and H. echinata genomes with guidance from the gene models respectively using HISAT2. BigWig XY tracks display the aligned RNA-seq reads as quantitative data in an x/y plot.
Assembled Transcripts: StringTie * (e.g., 4c1, 16c1, 64c1, 24h1, BL1C, PB1C, etc.)	Transcripts from a H. symbiolongicarpus developmental time series with four stages (4 cell, 16 cell, 64 cell, and 24 hours) and a H. echinata polyp head regeneration experiment with two time points (presumptive blastema, PB, at 0h and blastema, BL, at 24h post head removal) were assembled using StringTie.
Hsym_LRv1	Transcripts from a low redundancy strand-specific H. symbiolongicarpus transcriptome assembly from a mixture of feeding and sexual polyps.
Hech_LRv1	Transcripts from a low redundancy strand-specific H. echinata transcriptome assembly from a mixture of feeding, sexual, and defensive polyps, and stolonal tissue.
Hsym_bulk cell	Transcripts from a bulk cell sorted RNA-seq dataset from two reporter lines (Piwi1::GFP, Tfap2::GFP) described in Dubuc et al. 2020.
Hech_Regeneration_Trinity	Transcripts from a H. echinata head regeneration transcriptome assembly including presumptive blastema (0 hour regeneration) and blastema (24 hour regeneration) samples.
PANNZER2	Annotation results generated by using AUGUSTUS Hydractinia protein models as input to PANNZER2.
AUGUSTUS	Hydractinia gene models predicted using AUGUSTUS.
MT	Hydractinia mitochondrial gene models determined manually.
MT_other_features	Additional Hydractinia mitochondrial genomic features predicted on the mitochondrial scaffold (e.g., inverted repeats, pseudogenes, and origins of replication)
rfam-detailed	Rfam predictions (all RNAs except tRNA) of each Hydractinia genome. Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements.
trna-detailed	tRNA Rfam predictions of each Hydractinia genome. Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements.
6FRAMES_PFAM	Hydractinia protein domains derived from an hmmscan of the six-frame translations of each Hydractinia genome against the HMM database using an E-value cutoff of 1x10-6.
IP_PFAM	Protein domains derived from an hmmscan of the AUGUSTUS Hydractinia protein models against the HMM database using the InterProScan pipeline with default parameters.
InterProScan	InterProScan results from running the AUGUSTUS Hydractinia protein models through the InterProScan pipeline using default parameters.
PFAM	Protein domains derived from an hmmscan of the AUGUSTUS Hydractinia protein models against the HMM database using an E-value cutoff of 1x10-6.
BLASTP_augustus_vs_NR	BLASTP results from using AUGUSTUS Hydractinia protein models as queries against the NCBI nr protein database using an E-value cutoff of 1x10-5.
BLASTP_augustus_vs_UniProt	BLASTP results from using AUGUSTUS Hydractinia protein models as queries against the UniProt protein database using an E-value cutoff of 1x10-5.
Reference sequence	The Hydractinia genomic sequence and corresponding six-frame translations are depicted when fully zoomed-in.
All elements	Repetitive elements identified with the RepeatMasker de_novo pipeline using each Hydractinia genome as input.
DNA elements	The subset of DNA class of repetitive elements identified with the RepeatMasker de_novo pipeline using each Hydractinia genome as input.
LTR elements	The subset of LTR class of repetitive elements identified with the RepeatMasker de_novo pipeline using each Hydractinia genome as input.
MASK	Genomic regions that have been repeat-masked using RepeatMasker and RepeatModeler are highlighted in light blue.
SCF	Assembled genomic scaffolds (SCF) appear as solid black tracks with intermittent gaps shaded bright pink.