DOI: 10.5281/zenodo.17307475
title: AmarylOmicBase: An integrated transcriptome database for comparative analysis of Amaryllidoideae species

description: General description

Compiled database of transcriptome assemblies (previously published or de novo assembled in this study), transcriptome annotation and expression quantification for 29 Amaryllidoideae species: Amaryllis belladonna, Clivia miniata, Crinum asiaticum, Crinum x powellii, Galanthus elwesii, Galanthus sp., Hippeastrum sp., Hippeastrum striatum, Hippeastrum vittatum, Leucojum aestivum, Lycoris aurea, Lycoris chinensis, Lycoris incarnata, Lycoris longituba, Lycoris radiata, Lycoris sprengeri, Narcissus aff pseudonarcissus, Narcissus papyraceus, Narcissus pseudonarcissus, Narcissus Tête-à-Tête, Narcissus tazetta, Narcissus viridiflorus, Phycella aff cyrtanthoides, Rhodophiala pratensis, Scadoxus multiflorus, Traubia modesta, Zephyranthes candida, Zephyranthes carinata, Zephyranthes treatiae.

Data includes transcriptome assemblies, Transdecoder predictions of peptide sequences (along with GFF3 and BED files), expression quantification (count and TPM matrices for genes and trinity isoforms obtained with Kallisto), and annotation results (from EggNOG, Pfam, Uniprot Swissprot and Rfam), as well as signal peptide and transmemberane domain predictions (from SignalP and TmHMM). Annotations were compiled into a report for each species using Trinotate.

For Lycoris aurea, there are two assemblies and corresponding files: Lycoris_aurea_PB and Lycoris_aurea_TH. The first was constructed solely with long-read sequencing data (PacBio, PB); while the second was constructed with short reads using Trinity, with long-read assembly being used for scaffolding step of Trinity (Trinity Hybrid, TH).

File descriptions

All unitigs and predicted protein sequences are prefixed with an acronym to identify the species:




Species
Acronym


Amaryllis belladonna
Ambel


Clivia miniata
Clmin


Crinum asiaticum
Crasi


Crinum x powellii
Crpow


Galanthus elwesii
Gaelw


Galanthus sp.
Gasp


Hippeastrum sp.
Hisp


Hippeastrum striatum
Histr


Hippeastrum vittatum
Hivit


Leucojum aestivum
Leaes


Lycoris aurea PB
Lyaur


Lycoris aurea TH
Lyaur


Lycoris chinensis
Lychi


Lycoris incarnata
Lyinc


Lycoris longituba
Lylon


Lycoris radiata
Lyrad


Lycoris sprengeri
Lyspr


Narcissus aff pseudonarcissus
Naafps


Narcissus papyraceus
Napap


Narcissus pseudonarcissus
Napse


Narcissus Tête-à-Tête
NptatI


Narcissus tazetta
Nataz


Narcissus viridiflorus
Navir


Phycella aff cyrtanthoides
Phafcyr


Rhodophiala pratensis
Rhpra


Scadoxus multiflorus
Scmul


Traubia modesta
Trmod


Zephyranthes candida
Zecan


Zephyranthes carinata
Zecar


Zephyranthes treatiae
Zetre




Files



Amaryllidoideae_annotation_report.tar.gz: 1 Tab delimited trinotate report per species containing annotation results (EggNOG, Pfam, Uniprot Swissprot and Rfam, SignalP and TmHMM), as well as GO TERMS and KEGG of Uniprot or Pfam matches. Columns containing multiple fields have them separated with ^ and multiple results for the same sequence are collapsed in a single cell and separated with `. Last two fields contain transcript and peptide sequences.

Amaryllidoideae_Assemblies_nt97.tar.gz: 1 fasta file for each species assembled de novo in this project (Clivia miniata, Hippeastrum sp., Hippeastrum vittatum, Lycoris aurea (PB and TH), Lycoris incarnata, Lycoris chinensis, Lycoris longituba, Lycoris sprengeri, Lycoris radiata, Narcissus tazetta and Zephyranthes candida). These files were generated with Trinity followed by cd-hit est, discarding unitigs with less than 200 bp and with a similarity threshold of 0.97. They were used for pseudomapping with kallisto for a final filter to remove unitigs not expressed (artifacts).

Amaryllidoideae_bed.tar.gz: 1 BED file per species generated with Transdecoder predict (using blastp against Uniprot and hmmscan against Pfam)

Amaryllidoideae_blastp_uniprot.tar.gz: 1 files per species in blast output format 6 (no header and tab delimited columns). Column names: qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, bitscore)

Amaryllidoideae_emapper_EggNOG.tar.gz: 1 files per species. Output from emapper (prefix.emapper_annotations - format described here)

Amaryllidoideae_expression.tar.gz: 4 files per species. Tab-delimited files with row names and headers. Row names are gene/unitig IDs, column names are SRA IDs.



Species_kallisto.gene.TPM.not_cross_norm

Species_kallisto.isoform.TPM.not_cross_norm

Species_kallisto.gene.counts.matrix

Species_kallisto.isoform.counts.matrix



Amaryllidoideae_gff3.tar.gz: 1 GFF3 file per species generated with Transdecoder predict (using blastp against Uniprot and hmmscan against Pfam)

Amaryllidoideae_hmmscan_PfamA.tar.gz: 1 file per species generated with hmmscan (option --domtblout, domain hits table). File has 22 white-space-delimited fields followed by a free text target sequence description. It has 3 commented lines at the top, the middle one containing the column names.

Amaryllidoideae_infernal.tar.gz: 1 file per species generated with infernal's cmscan (using the Trinotate wrapper). Table format 2 described in Infernal's user guid section 6  

Amaryllidoideae_proteome.tar.gz: 1 fasta file per species generated with Transdecoder predict (using blastp against Uniprot and hmmscan against Pfam)

Amaryllidoideae_signalp.tar.gz: 3 files per species generated with SignalP6



Species_output.gff3: tab delimited GFF3 file of predictions per sequence

Species_prediction_results.txt: tab delimited table with two comment lines, second one contains column names. 

Species_region_output.gff3: tab delimited GFF3 file of predictions per region (N, H and C regions).



Amaryllidoideae_tmhmm.tar.gz: 1 tab delimited file generated with tmhmm2 (format short, described in the software's guide tab)

Amaryllidoideae_transcriptome.tar.gz: 1 fasta file per species