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Protocols

Lepbase specifications

Information


Unique identifier OMICS_12064
Name Lepbase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Lepbase
  • person_outline Mark Blaxter
  • person_outline Reuben Nowell

Publications for Lepbase

Lepbase citations

 (8)
library_books

Conservation and lineage specific rearrangements in the GOBP/PBP gene complex of distantly related ditrysian Lepidoptera

2018
PLoS One
PMCID: 5806886
PMID: 29425254
DOI: 10.1371/journal.pone.0192762

[…] base (P. xylostella, http://iae.fafu.edu.cn/DBM/; http://dbm.dna.affrc.go.jp/px/), Manduca Base (M. sexta, currently closed), MonarchBase (D. plexippus, http://monarchbase.umassmed.edu/home.html) and LepBase (other species, http://ensembl.lepbase.org/index.html). When no CDSs showed significant similarities, additional TBLASTN searches were performed against assembled genome sequences of the datab […]

library_books

De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)

2018
PMCID: 5958680
PMID: 29785409
DOI: 10.1016/j.dib.2018.01.073

[…] otential long non-coding RNAs and sequences for which the CDS was either too fragmented (n = 15,132) or not present at all (n = 55). Further comparative analysis of the reference transcripts with the Lepbase reference protein set detected probable homologs for 20,835 transcripts. OHR analyzes on the best matches indicated that 61% of the CDS were reconstructed at least at 60% of the correspondin […]

library_books

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera

2017
BMC Genomics
PMCID: 5712127
PMID: 29197336
DOI: 10.1186/s12864-017-4293-2

[…] re chosen to maximize species distribution across the full phylogenetic breadth of Lepidoptera, while also utilizing the most comprehensively annotated genomes based on published CEGMA scores (http://lepbase.org, []). Taxonomically restricted proteins were defined as those identified repeatedly across a given phylogenetic range but without homology in any outgroup species. Proteins exhibiting disc […]

library_books

Impact of Lateral Transfers on the Genomes of Lepidoptera

2017
Genes
PMCID: 5704228
PMID: 29120392
DOI: 10.3390/genes8110315

[…] epidoptera, although such integration events seem quite possible. Traces of viral p74, helicase 2 or helicase homologues can be found in D. plexippus or P. glaucus genomes using BlastP search against Lepbase (http://blast.lepbase.org/), and the phylogenetic analyses suggest that these genes were possibly acquired from a nudivirus (data not shown). Finally, while it is relatively easy to identify c […]

library_books

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood White (Leptidea) Butterflies

2017
Genome Biol Evol
PMCID: 5737376
PMID: 28981642
DOI: 10.1093/gbe/evx163

[…] es (Bombyx mori, Calycopis cecrops, Danaus plexippus, Heliconius melpomene, Lerema accius, Manduca sexta, Melitaea cinxia, Papilio glaucus, Papilio polytes, and Papilio xuthus) were obtained from the Lepbase database (http://www.lepbase.org; last accessed June 9, 2017, ) and the genome sequences of two additional species, Phoebis sennae and Pieris rapae, were obtained from the web repository: http […]

library_books

Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome

2017
Mol Biol Evol
PMCID: 5850747
PMID: 28957502
DOI: 10.1093/molbev/msx190

[…] P. interpunctella () was provided by Peter Harrison. We used the published transcriptome rather than the genome, which has not been published yet but is available on Lepidoptera Base (http://ensembl.lepbase.org/Plodia_interpunctella_v1/Info/Index), because there is no linkage information for the genome and to make our analyses comparable to those of . Plodia interpunctella transcripts () were fir […]

Citations

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Lepbase institution(s)
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK; Department of Genetics, Evolution and Environment, University College London, London, UK; Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands; Department of Zoology, Stockholm University, Stockholm, Sweden; Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland; Institute of Integrative Biology, University of Liverpool, Liverpool, UK; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Department of Biological Sciences, National University of Singapore, Singapore; Yale-NUS College, Singapore; Department of Zoology, University of Cambridge, Cambridge, UK
Lepbase funding source(s)
Supported by the ERC Advanced Grant number 250325 (EMARES) and by the South East Asian Biodiversity Genomics Center (NUS grants R-154-000-648-646 and R-154-000- 648-733) by BBSRC grant number BB/K020161.

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