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. 2019 Jul 23;10:654. doi: 10.3389/fgene.2019.00654

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Copyright © 2019 Hoang, Furtado, Perlo, Botha and Henry

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Transcriptome quality assessment via BUSCO, OrthoMCL, and Cogent packages. (A) BUSCO completeness assessment of two datasets, combined data and three reference transcriptome databases, SoGI, unigenes, and SUGIT. In the bar charts, C, S, D, F, and M denote complete, single, duplicate, fragmented, and missing BUSCOs. (B) Venn diagram showing BUSCOs recovered in each of datasets. (C) Number isoforms per gene family identified by Cogen pipeline. (D) Length distribution of extracted ORF sequences from the two datasets. (E) Venn diagram showing a comparison of orthologous groups between two datasets. (F) Long noncoding transcripts identified in the NO dataset (NO_lnc) compared against the unique fraction of transcripts from the NO dataset (NO_uni). NN, sugarcane non-normalized PacBio Iso-Seq isoforms; NO, sugarcane normalized PacBio Iso-Seq isoforms; SoGI, Saccharum officinarum gene indices; SUGIT, sugarcane Iso-Seq transcriptome; aa denotes amino acid.