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De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus.
Gigascience. 2016; 5:6.G

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.

FINDINGS

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+Show Affiliations

Plant Physiology and Genetics Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye Pacific Basin Agricultural Research Center, USDA Agricultural Research Services, Hilo, HI USA.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.Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ USA.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26823975

Citation

Tassone, Erica E., et al. "De Novo Construction of an Expanded Transcriptome Assembly for the Western Tarnished Plant Bug, Lygus Hesperus." GigaScience, vol. 5, 2016, p. 6.
Tassone EE, Geib SM, Hall B, et al. De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus. Gigascience. 2016;5:6.
Tassone, E. E., Geib, S. M., Hall, B., Fabrick, J. A., Brent, C. S., & Hull, J. J. (2016). De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus. GigaScience, 5, 6. https://doi.org/10.1186/s13742-016-0109-6
Tassone EE, et al. De Novo Construction of an Expanded Transcriptome Assembly for the Western Tarnished Plant Bug, Lygus Hesperus. Gigascience. 2016;5:6. PubMed PMID: 26823975.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - De novo construction of an expanded transcriptome assembly for the western tarnished plant bug, Lygus hesperus. AU - Tassone,Erica E, AU - Geib,Scott M, AU - Hall,Brian, AU - Fabrick,Jeffrey A, AU - Brent,Colin S, AU - Hull,J Joe, Y1 - 2016/01/28/ PY - 2015/09/04/received PY - 2016/01/06/accepted PY - 2016/1/30/entrez PY - 2016/1/30/pubmed PY - 2016/10/19/medline KW - Lygus hesperus KW - Miridae KW - Plant bug KW - RNA-Seq KW - Transcriptome KW - Trinity SP - 6 EP - 6 JF - GigaScience JO - Gigascience VL - 5 N2 - 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. FINDINGS: 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. SN - 2047-217X UR - https://www.unboundmedicine.com/medline/citation/26823975/De_novo_construction_of_an_expanded_transcriptome_assembly_for_the_western_tarnished_plant_bug_Lygus_hesperus_ DB - PRIME DP - Unbound Medicine ER -