MOESM2 of Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters

Additional file 2: Table B1. Genome annotation of the complete QM6a genomes, including AT-rich blocks, predicted genes, repetitive features, gene ontology (GO), gene names in T. reesei, Saccharomycetes cerevisiae and Neurospora crassa, as well as gene identity numbers in QM6a-v2.0 and RUT-C30-v1.0. (Columns A-H) All the genes that were not annotated in QM6a-v.20 and Rut-C30-v1.0 are highlighted with yellow background, whereas those only annotated in Rut-C30-v1.0 are highlighted with yellow-green background. (Columns O-AE) Comparative transcriptomic analysis of all QM6a genes in different carbon sources using two published transcriptome datasets: (1) The SOLiD sequencing reads from QM9a grown first in glucose for 48 hours, then in straw for 24 hours and finally with the addition of glucose for 5 hours [24]; (2) The Illumina HiSeq 2000 sequencing reads from QM9414 treated with cellulose (24, 48 and 72 hours), sophorose (2, 4 and 6 hours) and glucose (24 and 48 hours) [25]. The TPM values are shown. Table B2. Annotation of the complete QM6a genome. All the annotated QM6a genes are compared to those in QM6a-v2.0, Rut-C30-v1.0, all Trichoderma reesei proteins from NCBI, the QM6a-HiC annotation results by Druzhinina et al. [18], the annotation results by Schmoll et al. [4], as well as the BLAST results from Uniprot, NCBI non-redundant (nr) database, Fusarium fujikuroi (JGI), Sordaria macrospora (NCBI), Saccharomyces cerevisiae (SGD) and Schizosaccharomyces pombe (PomBase and NCBI). The e-values of all BLASTP results were < 1.0 x 10-5. Table B3. TPM values of all new QM6a genes revealed by two publicly-available transcriptome datasets [24, 25]. Table B4. Locations of 62 previously identified CAZyme and SSCP gene clusters [18] in 42 chromosomal blocks of the complete QM6a genome. All previously annotated QM6a-v2.0 or QM6a-HiC genes in these gene clusters are indicated in blue. AT-rich islands in these 42 chromosomal blocks are indicated in red. All new QM6a genes we identified in the complete QM6a genome are indicated in darkgreen.