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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #397904

Research Project: Healthy, Sustainable Pecan Nut Production

Location: Fruit and Tree Nut Research

Title: An updated de novo transcriptome for green ash (Fraxinus pennsylvanica)

item Brungardt, Jordan
item Bock, Clive

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2023
Publication Date: 4/18/2023
Citation: Brungardt, J.J., Bock, C.H. 2023. An updated de novo transcriptome for green ash (Fraxinus pennsylvanica). Genes, Genomes, Genetics. 13(6).

Interpretive Summary: The underlying genes of a genome are responsible for the production of different types of cells and tissues as well as when responding to different types of stress such as heat stress. Knowing the total amount of genes a particular organism can express is the first step for identifying genes that are important to these developmental and adaptive responses. This paper not only gives an improved understanding of the genes present and expressed in Green ash (Fraxinus pennsylvanica), but also highlights pitfalls present when identifying the complete set of genes expressed for any organism. Information from this research will surely help determine natural mechanisms used for fighting of a parasitic insect, Emerald ash borer, that is responsible for extinction level pressure for this tree.

Technical Abstract: De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for non-model species. Transcriptomes generated by this method can have large amounts of variability due to endless combinations of user defined variables and programs available for assembly. Many methods have been developed for evaluating the quality of these assemblies. Here, raw sequencing information for Green ash (Fraxinus pennsylvanica Marshall) that was previously published has been re-evaluated. An updated assembly has been developed by including additional sequencing information in combination with more stringent trimming parameters. Input reads were assembled with Trinity and Trans-Abyss assembly programs. The resulting Trinity assembly has a 7.3-fold increase in genomic breadth of coverage, a 2.4-fold increase in predicted complete open reading frames, an increased L50 value, and increased BUSCO completeness compared to the earlier published transcriptome.