Genome Browser

Browse the Hydra 2.0 genome assembly, protein models, RNA-seq data, and other genome annotation using the JBrowse genome viewer.

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The genome browser is searchable using a Hydra 2.0 scaffold or gene identifier. Note that scaffold names take the form Sc4wPfr_X, where “X" is a non-padded number (e.g., Sc4wPfr_97, Sc4wPfr_4397), and gene identifiers take the form “Sc4wPfr_X.gX.tX” (e.g., Sc4wPfr_97.g13.t1, Sc4wPfr_4397.g7.t1).

          

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The following tracks are currently available for viewing:

Aligned ATAC-seq tracks

Aligned ATAC-seq reads as quantitative data in an x/y plot. ATAC-seq reads (replicate 1, 2, and 3) were generated for whole homeostatic Hydra. The Juliano_whole_peaks track is a consensus peak track consisting of all peaks that passed an IDR threshold of 0.1 for at least one pairwise comparison among the three biological replicates (Juliano_whole_rep1-3).

Aligned ATAC-seq reads from Murad et al. 2019 from adult tissues and regeneration time points 0-48h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.

Aligned ChIP-seq tracks

Aligned ChIP-seq reads from Murad et al. 2019 from whole Hydra, Hydra head and regeneration time points 0-24h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.

Aligned RNA-seq tracks

RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0-48h were aligned to the Hydra 2.0 genome using HISAT2. Aligned reads tracks display all aligned RNA-seq reads. BigWig XY tracks display the aligned RNA-seq reads as quantitative data in an x/y plot.

Aligned RNA-seq reads from Murad et al. 2019 from adult Hydra hypostome, tentacles, body column, budding zone and foot, also from regeneration time points 0-48h and budding stages 1-10. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.

Juliano_Trinity

RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. The Trinity assembled transcripts were aligned to the Hydra (2.0) genome using Splign.

Juliano_aepLRv2

Transcripts from a transcriptome assembly for Hydra vulgaris AEP (38,749 transcripts) were aligned to the Hydra 2.0 genome using Splign.

Petersen_Trinity

RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0–12 h were used to assemble a de novo transcriptome, which consists of 36,338 high quality transcripts. The Trinity assembled transcripts were aligned to the Hydra (2.0) genome using Splign.

AUGUSTUS

Hydra 2.0 gene models predicted using AUGUSTUS.

AUGUSTUS_unmasked

Hydra 2.0 gene models predicted using AUGUSTUS with the unmasked genome.

FGENESH

Hydra 2.0 gene models predicted using FGENESH.

PASA

RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. Transcripts were used to create gene structures based on spliced alignments with PASA.

Hydra1.0_JGI

Hydra 1.0 gene models (from JGI) aligned to the Hydra 2.0 genome assembly using Splign.

Hydra1.0_NCBI

Hydra 1.0 gene models (from NCBI) aligned to the Hydra 2.0 genome assembly using Splign.

BLASTP_augustus_vs_NCBI_nr

BLASTP results from using AUGUSTUS protein models as queries against the NCBI nr protein database with an e-value cutoff of 1e-5.

BLASTP_augustus_vs_UniProt

BLASTP results from using AUGUSTUS protein models as queries against the UniProt protein database with an e-value cutoff of 1e-5.

PASA_coding_regions

Candidate coding regions identified from PASA gene structures by TransDecoder.

AUGUSTUS_PFAM

Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the AUGUSTUS datasets.

6FRAMES_PFAM

Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the six-frame translations of the Hydra 2.0 genome.

Reference Sequence

The Hydra 2.0 genomic sequence and corresponding six-frame translations depicted when fully zoomed-in.

MASK

Genomic regions that have been 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.