RNA-seq-Based Transcriptome Assembly for Sweet Corn

RNA-seq data was also generated for endosperm sampled 14 days after pollination. The total RNA was extracted using RNeasy MinElute (Qiagen) following the manufacturer’s recommended protocol. The total RNA was processed using the TruSeq RNA Sample Preparation kit followed by sequencing on the Illumina HiSeq 2500 platform. The software Trimmomatic v0.36 was used to trim adapter sequences of RNA sequencing reads^{70 (link)}. The paired-end reads were merged using PEAR v0.9.6^{71 (link)}, which were used for following transcriptome assembly. The de novo transcriptome assembly was performed using Trinity v2.8.4 with default parameters^{72 (link)}. The genome-guided transcriptome assembly was performed with HISAT2 v2.1.0^{73 (link),74 (link)} and StringTie v1.3.4^{75 (link)}. The genome index was built using HISAT2-build and the clean transcriptome reads were mapped to the sweet corn genome using HISAT2. The genome-guided transcriptome assembly was performed using StringTie. The resulting StringTie and Trinity assemblies were supplied to PASA v2.2.0^{76 (link)} in order to build comprehensive transcriptome database.

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Hu Y., Colantonio V., Müller B.S., Leach K.A., Nanni A., Finegan C., Wang B., Baseggio M., Newton C.J., Juhl E.M., Hislop L., Gonzalez J.M., Rios E.F., Hannah L.C., Swarts K., Gore M.A., Hennen-Bierwagen T.A., Myers A.M., Settles A.M., Tracy W.F, & Resende MF J.r. (2021). Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12, 1227.

Publication 2021

RNeasy MinElute TruSeq RNA Sample Preparation kit HiSeq 2500

Corn Endosperm Genome Pear Pollination Rna seq Transcriptome

Corresponding Organization :

Other organizations : University of Florida, Cold Spring Harbor Laboratory, Cornell University, Iowa State University, University of Wisconsin–Madison, Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences

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independent variables

RNA-seq data was also generated for endosperm sampled 14 days after pollination
The total RNA was extracted using RNeasy MinElute (Qiagen) following the manufacturer's recommended protocol
The total RNA was processed using the TruSeq RNA Sample Preparation kit
The software Trimmomatic v0.36 was used to trim adapter sequences of RNA sequencing reads
The paired-end reads were merged using PEAR v0.9.6
The de novo transcriptome assembly was performed using Trinity v2.8.4 with default parameters
The genome-guided transcriptome assembly was performed with HISAT2 v2.1.0 and StringTie v1.3.4

dependent variables

Transcriptome assembly

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

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