title: De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus.
abstract: BACKGROUND
  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 the biology of this species. Earlier Lygus transcriptome assemblies were limited by low read depth, or because they 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.
  
  
  RESULTS
  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 2075 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 the new assembly's utility revealed that the length and abundance of transcripts predicted to regulate insect physiology and chemosensation have improved, compared with previous L. hesperus assemblies.
  
  
  CONCLUSIONS
  This transcriptome represents a significant expansion of Lygus transcriptome data, and improves foundational knowledge about the molecular mechanisms underlying L. hesperus biology. The dataset is publically available in NCBI and GigaDB as a resource for researchers.
authors.affiliation: Plant Physiology and Genetics Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.
authors.forename: Erica E
authors.initials: EE
authors.lastname: Tassone
authors.affiliation: Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye Pacific Basin Agricultural Research Center, USDA Agricultural Research Services, Hilo, HI USA.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Geib
authors.affiliation: Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye Pacific Basin Agricultural Research Center, USDA Agricultural Research Services, Hilo, HI USA ; Department of Plant and Environmental Protection Sciences, University of Hawaii Manoa, Honolulu, HI USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Hall
authors.affiliation: Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Fabrick
authors.affiliation: Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.
authors.forename: Colin S
authors.initials: CS
authors.lastname: Brent
authors.affiliation: Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.
authors.forename: J Joe
authors.initials: JJ
authors.lastname: Hull
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D063990:Gene Ontology; D017344:Genes, Insect / Q000235:genetics*; D005837:Genitalia, Male / Q000378:metabolism; D020062:Heteroptera / Q000235:genetics* / Q000502:physiology; D006790:Host-Parasite Interactions; D008297:Male; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D010935:Plant Diseases / Q000469:parasitology; D010944:Plants / Q000469:parasitology; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Lygus hesperus; Miridae; Plant bug; RNA-Seq; Transcriptome; Trinity
references.citation: PLoS One. 2014 Nov 17;9(11):e113046
references.pmid: 25401762
references.citation: Gigascience. 2015 Mar 31;4:14
references.pmid: 25830018
references.citation: Bioinformatics. 2014 May 1;30(9):1236-40
references.pmid: 24451626
references.citation: J Insect Physiol. 2014 Jan;60:104-10
references.pmid: 24333151
references.citation: PLoS One. 2013;8(1):e55105
references.pmid: 23357950
references.citation: Bioinformatics. 2015 Oct 1;31(19):3210-2
references.pmid: 26059717
references.citation: Insect Biochem Mol Biol. 2016 Feb;69:71-81
references.pmid: 26003917
references.citation: BMC Bioinformatics. 2011 Aug 04;12:323
references.pmid: 21816040
references.citation: Peptides. 2014 Mar;53:125-33
references.pmid: 23932938
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D729-34
references.pmid: 22135296
references.citation: Nat Protoc. 2013 Aug;8(8):1494-512
references.pmid: 23845962
references.citation: Gigascience. 2016 Jan 28;5:6
references.pmid: 26823975