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De-novo SuperTranscriptome assembly from the nodal root growth zone of maize inbred line FR697


Sidharth Sen







Certain cultivars of maize show increased resistance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaption, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de-novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated from various FR697 plant tissue samples. The Necklace pipeline was used to combine a Trinity de-novo assembly along with a reference guided assembly and the Viridiplantae proteome to generate an annotated consensus “SuperTranscriptome” assembly of 47915 transcripts with a N50 of 3152 bp in length. The results were compared by Blastn to maize reference genes, a BUSCO genome completeness report, and compared with three maize reference genomes.

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