Supporting data and materials from "Transcriptome of the egg parasitoid Fopius arisanus, an important biocontrol tool for Tephritid fruit fly suppression".
Dataset type: Transcriptomic
Data released on August 05, 2015
The Braconid wasp Fopius arisanus (Sonan) has been utilized for biological control of the Mediterranean fruit fly (Ceratitis capitata), and the oriental fruit fly (Bactrocera dorsalis), both of which are phytophagous fruit fly pests of economic importance in Hawaii. We have sequenced and assembled the transcriptome of this wasp using tissue from four different life stages: larvae, pupae, adult males and adult females, with the aim to contribute foundational resources to aid in the understanding of the biology and behavior of this important parasitoid. The transcriptome of the parasitic wasp Fopius arisanus was sequenced and reconstructed using a strategy that identified 15,346 high confidence, non-redundant transcripts derived from 8,307 predicted unigenes. In addition, Pfam domain annotations were detected in 78% of these transcripts. The distribution of transcript length is comparable to that found in other hymenoptera genomes. Through orthology analysis, 7,154 transcripts were identified as having orthologs in at least one of the four other hymenopteran parasitoid species examined. Approximately 4,000 core orthologs were found to be shared between F. arisanus and all four of the other parasitoids. E12Availability of high quality genomic data is fundamental for the improvement and advancement of research in any biological organism. Parasitic wasps are important in the biological control of agricultural pests. The transcriptome data presented here represent the first large-scale molecular resource for this species, or any closely related Opiine species.
Additional details
Read the peer-reviewed publication(s):
- Calla, B., Sim, S. B., Hall, B., DeRego, T., Liang, G. H., & Geib, S. M. (2015). Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0075-4
Additional information:
http://genomeannotation.github.io/
Accessions (data included in GigaDB):
BioProject: PRJNA259570
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
---|---|---|---|---|---|
Fari_larvae | Fopius arisanus | Tissue:whole organism Subspecific genetic lineage:USDA-PBARC Fari_Bdor Sex:mixed ... |
64838 | ||
Fari_pupae | Fopius arisanus | Life stage:pupae Description:pooled F. arisanus pupae of varying ag... Sex:mixed ... |
64838 | ||
Fari_adultMale | Fopius arisanus | Age:mixed Subspecific genetic lineage:USDA-PBARC Fari_Bdor Alternative accession-BioSample:SAMN03010495 ... |
64838 | ||
Fari_adultFemale | Fopius arisanus | Sex:female [PATO:0000383] Life stage:adult Subspecific genetic lineage:USDA-PBARC Fari_Bdor ... |
64838 |
Click on a table column to sort the results.
Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
---|---|---|---|---|---|---|---|---|
Unfiltered Trinity RNAseq assembly of all sampled (command: Trinity --seqType fq --JM 65 --left ../RawData/*.R1*fastq --right ../RawData/*.R2*fastq --CPU 32 --jaccard_clip --normalize_reads --normalize_max_read_cov 50 --min_kmer_cov 1 --bflyCalculateCPU --bflyHeapSpaceInit 4G) , release r2014_07-17 | Transcriptome sequence | FASTA | 128.14 MB | 2015-07-27 | MD5 checksum: d4fca914c38db8c8dc3155ee2f582ab2 |
|||
Blastx results of unfiltered Trinity.fasta file against Uniprot_swissprot database (command: blastx -query Trinity.fasta -db uniprot_sprot -out blastx.outfmt6 -evalue 1e-20 -num_threads 32 -max_target_seqs 1 -outfmt 6 | Other | UNKNOWN | 1.84 MB | 2015-07-27 | MD5 checksum: 7e01ab9cebce8e94abb4927b7c16b77f |
|||
Transdecoder output of predicted peptides in unfiltered Trinity.fasta, with Pfam search (command: TransDecoder -t Trinity.fasta --search_pfam /data0/opt/BlastSoftware/DB/Pfam-A.hmm --CPU 32) | Protein sequence | FASTA | 24.29 MB | 2015-07-27 | MD5 checksum: 85cf902c599e55610883d86fb04c6aa1 |
|||
Blastp results of unfiltered Trinity.fasta file against Uniprot_swissprot database (command: blastp -query Trinity.fasta.predicted.peps -db uniprot_sprot -out blastx.outfmt6 -evalue 1e-20 -num_threads 32 -max_target_seqs 1 -outfmt 6 | Other | FASTA | 3.63 MB | 2015-07-27 | MD5 checksum: e60e61f11b81daf5eb00998421ea0adb |
|||
InterProScan results (version 5.3-46.0) results of unfiltered predicted proteins (command: interproscan.sh --goterms --iprlookup -pa -i input.faa -b out) | Tabular data | UNKNOWN | 73.26 MB | 2015-07-27 | MD5 checksum: 0d55d306ce99328062eb6a3f001fb787 |
|||
RSEM abundance estimation at unigene level (run through trinity untility script: align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left all.R1.fastq --right all.R2.fastq --est_method RSEM --aln_method bowtie --thread_count 32 --trinity_mode --prep_reference), all reads concatenated into single sample | Tabular data | UNKNOWN | 3.41 MB | 2015-07-27 | MD5 checksum: df40691adfbe02acbb788991f9ac252b |
|||
RSEM abundance estimation at isoform level (run through trinity untility script: align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left all.R1.fastq --right all.R2.fastq --est_method RSEM --aln_method bowtie --thread_count 32 --trinity_mode --prep_reference), all reads concatenated into single sample | Tabular data | UNKNOWN | 4.88 MB | 2015-07-27 | MD5 checksum: e3ded00646f55ab9c92c4fa1766a4dec |
|||
OrthoMCL results "inparalogs" | Tabular data | TEXT | 1.02 MB | 2015-07-27 | MD5 checksum: 5b17db738920dbfe8b1e07c5e09aca1c |
|||
OrthoMCL results "orthologs" | Tabular data | TEXT | 5.01 MB | 2015-07-27 | MD5 checksum: d6bea32c009e2dd309168e270fa5ea92 |
|||
OrthoMCL results "coorthologs" | Tabular data | TEXT | 615.36 kB | 2015-07-27 | MD5 checksum: dededf289bf71a6b812a528366807f1f |
Date | Action |
---|---|
August 10, 2015 | Dataset publish |
September 4, 2015 | Sample taxon ID changed |
September 4, 2015 | Sample taxon ID changed |
September 4, 2015 | Sample taxon ID changed |
September 4, 2015 | Sample taxon ID changed |
February 3, 2016 | External Link removed : http://moana.dnsalias.org/~sgeib/Bcur_RNAseq_Trinity/ |