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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

Calla B; Sim SB; Hall B; DeRego T; Liang G; Geib SM (2015): Supporting data and materials from "Transcriptome of the egg parasitoid Fopius arisanus, an important biocontrol tool for Tephritid fruit fly suppression". GigaScience Database. https://doi.org/10.5524/100158

DOI10.5524/100158

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.

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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

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Table Settings
Sample 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

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Table Settings

File 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/