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Data released on January 22, 2016

Supporting data for "De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus".

Brent, C, S; Fabrick, J, A; Geib, S, M; Hall, B; Hull, J, J; Tassone, E, E (2016): Supporting data for "De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus". GigaScience Database. http://dx.doi.org/10.5524/100172 RIS BibTeX Text

The plant bug, Lygus hesperus Knight, is a polyphagous pest of many economically important crops. Despite its pest status, little is known about the molecular mechanisms responsible for much of Lygus biology. Earlier Lygus transcriptome assemblies were either limited by low read depth or focused on specific conditions. To generate a more comprehensive transcriptome, we supplemented previous datasets with new reads corresponding to specific tissues (heads, antennae, and male reproductive tissues). This transcriptome augments current Lygus molecular resources and provides the foundational knowledge critical for future comparative studies.
An expanded, Trinity-based de novo transcriptome assembly for L. hesperus was generated using previously published whole body Illumina data supplemented with 293 million bp of new raw sequencing data corresponding to five tissue-specific cDNA libraries and 11 Illumina sequencing runs. The updated transcriptome consists of 22,022 transcripts (average length of 2,075 nt), 62% of which contain complete open reading frames. Significant coverage of the BUSCO (benchmarking universal single-copy orthologs) dataset and robust metrics indicate that the transcriptome is a quality assembly with a high degree of completeness. Initial assessment of assembly utility revealed that the length and abundance of transcripts predicted to regulate insect physiology and chemosensation have improved with the new assembly compared to previous L. hesperus assemblies.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0109-6

Accessions (data included in GigaDB):

BioProject: PRJNA284294
BioProject: PRJNA238835
BioProject: PRJNA210219
BioProject: PRJNA210220

Transcriptomic

http://gigadb.org/images/data/cropped/100172.jpg

Funding:

  • Funding body - Cotton Inc.
  • Award ID - project no. 12-373
  • Comment - Colin S Brent
  • Funding body - National Science Foundation
  • Award ID - OCI-1053575XSEDE
  • Comment - allocation TG-MCB140032 Scott M Geib

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN0222216030085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:6 to 9
Sex:female
...
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SAMN0222216130085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:6 to 9
Sex:female
...
+
SAMN0222216230085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:6 to 9
Sex:male
...
+
SAMN0222216330085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:6 to 9
Sex:male
...
+
SAMN0222216430085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:not recorded
Sex:male
...
+
SAMN0222216530085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:not recorded
Sex:male
...
+
SAMN0222216630085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:not recorded
Sex:male
...
+
SAMN0222216730085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:not recorded
Sex:male
...
+
SAMN0267994030085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:10
Sex:female
...
+
SAMN0267994130085 lygus bugLygus hesperus Description:derived from a L. hesperus laboratory ...
Age:10
Sex:female
...
+
Displaying 1-10 of 20 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 
Tabular dataUNKNOWN4.82 MB2016-01-04
Transcriptome sequenceFASTA43.93 MB2016-01-04
TextUNKNOWN0.84 KB2016-01-04
TextUNKNOWN0.19 KB2016-01-04
TextUNKNOWN6.22 MB2016-01-04
AnnotationGFF20.11 MB2016-01-04
Coding sequenceFASTA122.93 KB2016-01-04
Coding sequenceFASTA48.62 KB2016-01-04
ReadmeTEXT2.21 KB2016-01-04
Protein sequenceFASTA26.56 KB2016-01-04
Displaying 1-10 of 13 File(s).

History:

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