Long-read transcriptome data for improved gene prediction in Lentinula edodes.

Lentinula edodes

Immune supportGut & microbiome

SpeciesShiitake, Hua Gu

JournalData in brief

Year2017

Key points

Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan
The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking
To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb
Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction
Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters
The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788

Metadata-grounded summary

Citation abstract

Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb. Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction. Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters. The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788.

Citation

Park SG, Yoo SI, Ryu DS, Lee H, Ahn YJ, Ryu H, et al. (2017). Long-read transcriptome data for improved gene prediction in Lentinula edodes. Data in brief https://doi.org/10.1016/j.dib.2017.09.052 PMID: 29845094

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