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

Authors: Tassone, Erica; Geib, Scott; HALL, BRIAN - University Of Hawaii; Fabrick, Jeffrey; Brent, Colin; Hull, Joe

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2016
Publication Date: 1/28/2016
Publication URL: https://handle.nal.usda.gov/10113/61983
Citation: 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.

Interpretive Summary: The western tarnished plant bug is an important pest of numerous crops in the western United States. Despite its economic importance, little is currently known about the genes that influence the biology (e.g. growth, development, and interactions with the environment) of this bug. When a given gene is turned on it produces a chemical sequence (a transcript) that provides information to a cell to produce a protein that performs a specific function within that cell. The collective transcripts (a transcriptome) at a given time, age, or within a given organ or tissue reflect the specific genes that are expressed. We have previously generated transcriptome databases that contain information for several thousand gene products; however, those databases were largely defined based on whole adult bodies. To generate a more comprehensive database, we supplemented the initial databases with sequence information for genes expressed in heads, antennae, and male reproductive tissues. The new database represents a marked improvement over previous iterations by providing better quality information for more genes. These data provide base-line information to better document the underlying genetics of the western tarnished plant bug. This knowledge is essential to fully understand how this pest interacts with its agricultural environment, and will facilitate the development of improved biologically-based management strategies.

Technical 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 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 reads corresponding to specific tissues (heads, antennae, and male reproductive tissues). This expanded transcriptome offers greater insight into the molecular genetics of Lygus, and provides greater foundational knowledge from which comparative studies with other plant bugs can be made. Findings: A de novo transcriptome assembly was generated from multiple libraries comprising different tissues and thermal conditions. The transcriptome consists of 22,022 transcripts (average length of 2075 nt), 62% of which contain complete open reading frames. Transcriptome metrics are consistent with a robust assembly, with both CEGMA and BUSCO analyses showing a high degree of completeness. In addition, more transcripts with homology to genes encoding proteins/peptides critical to regulating insect physiology and chemosensation were identified in the current assembly than previous iterations. 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.