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
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
Nature Ecology & Evolution 2, 141–151
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_nge.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
| nge_genome_v2.0.fa.gz | genome assembly |
| nge_genome_v2.0_nucl.fa.gz | genemodel nucl |
| nge_genome_v2.0_prot.fa.gz | genemodel prot |
| nge_genome_v2.0_Swiss-Prot.outfmt6.gz | genemodel blastp (db: swiss prot) |
| nge_genome_v2.0_Pfam.domtblout.gz | genemodel pfam domain |
| 52_nge_v2.gff.gz | GFF file of the augustus annotation |
transcriptome version 2.0
| nge_transcriptome_nucl.fa.gz | transcriptome nucl |
| nge_transcriptome_prot.fa.gz | transcriptome prot |
| nge_transcriptome_Swiss-Prot.outfmt6.gz | transcriptom blastp (db: swiss prot) |