Phoronis australis ver. 2.0

OIST Marine Genomics Unit since 2008

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publication
For those who utilize our genome and transcriptome data, please cite:
Luo, Y.J., Kanda, M., Koyanagi, R., Hisata, K., Akiyama, T., Sakamoto, H., Sakamoto, T., Satoh, N.
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
Nature Ecology & Evolution 2, 141–151 Pubmed
1. Gene family analysis
Gene family analysis was conducted using all-to-all BLASTP searches against 31 selected metazoan proteomes (species_code.xlsx). Orthologous groups (OG) were then identified with OrthoMCL (v2.0.9) using a default inflation number (I = 1.5) for the Markov clustering. The file "groups.txt" provides the OrthoMCL results of gene family clustering in a plain text format Each line with OG IDs and gene IDS represents those genes are in the same gene family. We provide the OrthoMCL results and gene family ID lists as follows:
figure_2a.zip Gene families in Figure 2 (Bilaterian gene repertoire)
File name description:
Supplementary Data 1.xlsx, List of gene IDs and annotations in Figure 2a.
bilaterian_core.txt, 7,007 core bilaterian gene families
lan.groups.list, 13,158 gene families in Lingula
nge.groups.list, 14,396 gene families in Notospermus
obi.groups.list, 11,545 gene families in Octopus
pau.groups.list, 11,169 gene families in Phoronis
figure_S24.zip Gene families in Supplementary Figure 24 (Gene families shared by lophotrochozoans and deuterostomes)
File name description:
Supplementary Data 2.xlsx, List of gene IDs and annotations in Supplementary Figures 24a,b and 28a.
Supplementary Data 3.xlsx, List of gene IDs and annotated gene ontology (GO) enrichment terms in Supplementary Figure 24c–e. NA, not available. bilaterian_core.txt, 6,413 core bilaterian gene families
deuterostome.groups.list, 26,836 gene famlies in the deuterostome lineage
ecdysozoan.groups.list, 15,810 gene families in the ecdysozoan lineage
lophotrochozoan.groups.list, 32,795 gene families in the lophotrochozoan lineage
platyzoan.groups.list, 18,396 gene families in the platyzoan lineage
lophotrochozoan+deuterostome_humanID.list, 950 gene famlies shared by lophotrochozoans and deuterostomes with annotation based on human gene IDs
figure_S50.zip Toxin candidate genes in Supplementary Figure 50
File name description:
lan_BBH_to_toxin.txt, 64 putative toxin genes identified in Lingula
nge_BBH_to_toxin.txt, 63 putative toxin genes identified in Notospermus
obi_BBH_to_toxin.txt, 48 putative toxin genes identified in Octopus
pau_BBH_to_toxin.txt, 60 putative toxin genes identified in Phoronis
Format: First column, species gene IDs; Second column, Swiss-Prot reciprocal best hits

2. Microsynteny analysis
scripts.zip Perl scripts for gene family analysis.
tutorial The link provides a detailed step-by-step tutorial on microsynteny analysis.

Expression profiles
trans_counts_pau.TMM.EXPR.matrix.zip Expression profiles in trimmed mean of M-values (TMM)-normalized transcripts per million (TPM)

Gene family clustering results
groups.txt.zip 65,786 gene families clustered from 31 selected metazoan proteomes.
OrthoMCL and UniProt format: ("3-letter code in lowercase" + "|" + "unique gene ID" + "_" + "5-letter code in uppercase") e.g. hsa|BMP4_HUMAN, lan|14486_LINAN
species_code.xlsx.zip a list for the species code used in OrthoMCL ID format
groups.zip species_code.groups.list. gene families in a given species
singletons.zip species_code.singletons.list. orphan genes in a given species

genome version 2.0
pau_genome_v2.0.fa.gz genome assembly
pau_genome_v2.0_nucl.fa.gz genemodel nucl
pau_genome_v2.0_prot.fa.gz genemodel prot
pau_genome_v2.0_Swiss-Prot.outfmt6.gz genemodel blastp (db: swiss prot)
pau_genome_v2.0_Pfam.domtblout.gz genemodel pfam domain
51_pau_v2.gff.gz GFF file of the augustus annotation

transcriptome version 2.0
pau_transcriptome_nucl.fa.gz transcriptome nucl
pau_transcriptome_prot.fa.gz transcriptome prot
pau_transcriptome_Swiss-Prot.outfmt6.gz transcriptome blastp (db: swiss prot)

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