About this database

Polypedilum vanderplanki or the sleeping chironomid, is a dipteran in the family Chironomidae. It occurs in northern Nigeria and Uganda where its larvae grow in temporary pools of water that frequently dry out during the lifetime of P. vanderplanki larvae.

News

• Genome browser for ARIds was added. [25th Nov, 2013]
• Pv Fosmid-ends increased in number. The current number of Fosmid-end sequences is 7,009. [18th June, 2013]
• Database was updated [14th June, 2013]
  - Raw BLAST report file can be downloaded.
  - Pv Sanger ESTs were incorporated into DB.
  - Some bugs were fixed.
  
• The BLAST search was updated. Subject sequences can be downloaded as FASTA file by clicking "Download" button. [13th June, 2013]
• The 486 Pv Fosmid-ends were added to GBrowse.[12th June, 2013]
• Database was updated.[7th June, 2013]
  - The tentative BLAST interface was added. The interface will be improved in the next update.
  - The BLAST search form accepts only a simple text sequence. Please remove a definition line starts with ">" from FASTA format sequence.
• Dataset was updated to version 0.90. [24th May, 2013]
  - Scaffold IDs were modified for genome paper.
  - Scaffolds were filtered based on scaffold length and RPKM value of gene.
  - Genes filtering based on RPKM value was performed.
  - GBrowse was updated to provide the latest dataset.
  - Orthologous/paralogous and expression data was added to gene description page. Functional annotation data on gene description page was enriched.
  - Functionality of gene search was improved.

Contributing organizations

Gene search

BLAST

Select program: blastn blastx blastp tblastx tblastn

Nucleotide database for blastn|tblastn|tblastx [1]: Pv scaffolds Pn scaffolds Pv GeneModels (CDS) Pn GeneModels (CDS) Pv Fosmid-ends Pv Sanger ESTs

Nucleotide database for blastn|tblastn|tblastx [2]: A. gambiae (CDS) A. aegypti (CDS) D. melanogaster (CDS) C. quinquefasciatus (CDS)

Protein database for blastp|blastx: Pv GeneModel (AA) Pn GeneModel (AA) A. gambiae (AA) A. aegypti (AA) D. melanogaster (AA) C. quinquefasciatus (AA)

Expectation value: 10 1 0.1 0.01 0.001 1e-3 1e-5 1e-10 1e-20 1e-50

Complexity filter: Off On

# hits displayed: 10 50 100 250

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Download page

Data for genome paper

• Pv scaffolds v0.9 [List of Pv scaffolds in MS-Excel]
• Pn scaffolds v0.9 [List of Pn scaffolds in MS-Excel]
• Pv gene model v0.91 (FASTA file; 17,137 genes)
• Pn gene model v0.91 (FASTA file; 16,553 genes)
• Pv gene model v0.91 (GFF file; 17,137 genes)
• Pn gene model v0.91 (GFF file; 16,553 genes)

Genome data

P. vanderplanki WGS reads

• Roche 454 GS FLX Titanium single end reads
• Illumina GAIIx 7kb mate-pair reads (100bp x 2)
• Illumina GAIIx paired-end (100bp x 2)
• ABI SOLiD4 reads

P. nubifer WGS reads

• ABI SOLiD4 reads (fastq format)
• Illumina GAIIx paired-end (100bp x2)

Transcriptome data

P. vanderplanki

• RNA-Seq reads [PvD0; whole-body, desiccation 0h]
• RNA-Seq reads [PvD24; whole-body, desiccation 24h]
• RNA-Seq reads [PvD48; whole-body, desiccation 48h]
• RNA-Seq reads [PvR3; whole-body, rehydration 3h]
• RNA-Seq reads [PvR24; whole-body, rehydration 24h]
• RNA-Seq reads [PvLarva; whole-body, larva, paired-end]
• RNA-Seq reads [PvPupae; whole-body, pupae, paired-end]
• RNA-Seq reads [PvFemaleAdult; whole-body, female adult, paired-end]
• RNA-Seq reads [PvMaleAdult; whole-body, male adult, paired-end]

P. nubifer

• RNA-Seq reads [PnD0; whole-body, desiccation 0h]
• RNA-Seq reads [PnD24; whole-body, desiccation 24h]
• RNA-Seq reads [PnLarvae; whole-body, larvae, paired-end]

Assembled data

P. vanderplanki

• Assembled reads from 454 reads using Newbler Assembler
• Assembled data from Illumina reads using Velvet assembler (built by Moscow group)
• Scaffolds from Illumina and SOLiD4 reads using Platanus assembler

P. nubifer

• Assembled reads from 454 reads using Newbler Assembler
• Scaffolds from Illumina and SOLiD4 reads using Platanus assembler

Gene model

P. vanderplanki

• Nucleotide sequences (17,824 sequences)
• Amino acid sequences (17,824 sequences)
• GFF (General Feature Format) file (17,824 genes)
• Nucleotide sequences (with support data; 16,158 sequences)
• Amino acid sequences (with support data; 16,158 sequences)

P. nubifer

• Nucleotide sequences (17,224 sequences)
• Amino acid sequences (17,224 sequences)
• GFF (General Feature Format) file (17,224 genes)
• Nucleotide sequences (with support data; 15,426 sequences)
• Amino acid sequences (with support data; 15,426 sequences)

Publication

Members

National Institute of Agrobiological Sciences (NIAS)

• Takahiro Kikawada
• Richard Cornette
• Oleg Gusev
• Yoshitaka Suetsugu

Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST)

• Noriyuki Satoh
• Takeshi Kawashima
• Ryo Koyanagi
• Manabu Fujie

Belozersky Institute of Physico-Chemical Biology, Moscow State University

• Maria Logacheva
• Alexei Penin
• Alexei Kondrashev

Institute of Biology and Fundamental Medicine, Kazan Federal University

• Oleg Gusev
• Elena Sahimardanova

Moscow Institute of Physico-Chemical Medicine

• Dmitry Alexeev
• Maxim Belenkin
• Vadim Govorun

Contact us

If you have any questions, please send email to xxxxxxxxxxxxxx.