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Data released on November 27, 2017

Supporting data for "Genome assembly of the pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly-valued ecologically keystone Neotropical timber forest tree"

Silva-Junior, O, B; Grattapaglia, D; Novaes, E; Collevatti, R, G (2017): Supporting data for "Genome assembly of the pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly-valued ecologically keystone Neotropical timber forest tree" GigaScience Database. http://dx.doi.org/10.5524/100379 RIS BibTeX Text

Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the "new mahogany", it is the second most expensive timber and the most logged species in Brazil, under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber and to identify genes for important metabolic compounds.
The genome assembly covered 503.7Mb (N50=81,316 bp), 90.4% of the 557 Mbp genome, with 13,206 scaffolds. A repeat database with 1,508 sequences was developed allowing masking ~31% of the assembly. Depth of coverage indicated that consensus determination adequately removed haplotypes assembled separately due to the extensive heterozygosity of the species. Automatic gene prediction provided 31,688 structures and 35,479 mRNA transcripts, while external evidence supported a well-curated set of 28,603 high-confidence models (90% of total). Finally, we used the genomic sequence and the comprehensive gene content annotation to identify genes related to the production of specialized metabolites.
This genome assembly is the first well-curated resource for a Neotropical forest tree and the first one for a member of the Bignoniaceae family, opening exceptional opportunities to empower molecular, phytochemical and breeding studies. This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA324125

Keywords:

heterozygous genome rna-seq transposable elements quinoids bignoniaceae 

Genomic

http://gigadb.org/images/data/cropped/100379.jpg

Funding:

  • Funding body - Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • Award ID - 471366/2007-2
  • Awardee - Rosane Garcia Collevatti
  • Funding body - Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • Award ID - 457406/2012-7
  • Awardee - Rosane Garcia Collevatti
  • Funding body - Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • Award ID - Rosane Garcia Collevatti
  • Awardee - Evandro Novaes
  • Funding body - Fundação de Apoio à Pesquisa do Distrito Federal
  • Award ID - 193.000.570/2009
  • Comment - NEXTREE
  • Awardee - Dario Grattapaglia

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Himp-UFG1429701Handroanthus impetiginosus Description:DNA extracted from leaves of adult pla...
Alternative accession-BioSample:SAMN05195323
Molecular data type:DNA
...
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HIMP-UFG1-RNA-POOL429701Handroanthus impetiginosus Description:Total RNA from shoots of five seedling...
Alternative accession-BioSample:SAMN07346903
Molecular data type:RNA
...
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Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
annotationTEXT21.46 KB2017-11-13
annotationTEXT0.25 KB2017-11-13
annotationTEXT0.29 KB2017-11-13
Coding SequenceFASTA10.2 MB2017-11-13
ReadmeTEXT0.7 KB2017-11-13
transcriptome sequenceTSV937.71 KB2017-11-13
annotationTSV1.76 MB2017-11-13
annotationUNKNOWN4.07 MB2017-11-13
protein sequenceFASTA6.67 MB2017-11-13
Himp-UFG1Sequence assemblyFASTA140.1 MB2017-11-13
Displaying 1-10 of 16 File(s).

History:

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