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Pipeline publication

[…] ross these eight types, chiloglottone 1 production only occurs in the callus of the vmb and flw type under 2 h UV-B, with chiloglottone levels higher in the flw than the vmb stage. Three biological replicates were used for each pool of the eight types of treatment. A total of 533,355,046 paired-end reads 150 bp in length, equivalent to 160 gigabases of sequence data, were obtained. Removal of adapter and low-quality sequences results in 464,624,600 high-quality PE reads, which represented 87.1% of the total sequenced reads (Table ). Given the lack of C. trapeziformis genome, reconstruction of the floral transcriptome for the 464.6 M high-quality PE reads used a three-step strategy involving Trinity (), Bowtie (), and Corset (), producing 686,243 contigs in the preliminary assembly. The final assembly consists of 221,668 contigs retained by Corset (Supplementary Data , ) – effectively removing many short contigs (<200 bp) while retaining the ones that have strong read support and/or shared sequence similarity (Supplementary Figures ). In addition, Corset show that 221,668 contigs can be further clustered into 146,545 clusters (transcripts). Summary statistics of the final assembly shows the average length is approximately 1,301 bp, N50 score of 1,953 bp, and a GC content of 0.4, among others (Supplementary Figure )., Sequence similarity searches (RapSearch2) using TRAPID () revealed that significant protein hits were found for 88,454 contigs against the PLAZA reference proteome with top matches against Vitis vinifera (8,339), Oryza sativa ssp. indica (7,691), Brachypodium distachyon (7,266), Sorghum bicolor (6,899), and Glycine max (6,878) protein sequences (Supplementary Figure ). In addition, 87,219 (39.3%) contigs were assigned as full-length, quasi full-length, or partial, while 134,449 (60.7%) contigs has no information assigned. Of these, 118,423 contigs contained both start and stop codons, while 19,818 and 65,811 contigs contained only stop and stop codons, respectively (Supplementary Figure )., MapMan BIN categories () showed higher overall representation for protein (6,574), RNA (5,277), signaling (3,216), transport (2,642), DNA (1,837), and cell (1,666) categories amongst 34,650 (15.6%) annotated contigs (Supplementary Figure ). The remaining 187,018 contigs are unknown and therefore classified in the ‘not assigned unknown and no ontology’ category by Mercator. As alternative annotations, gene ontology (GO) or protein domain (InterPro) were also assigned to 72,970 (32.9%) and 78,560 (35.4%) contigs, respectively. A summary of assigned GO categories as plant GO Slim categories revealed that the cellular (21.1%) and metabolic (21.2%) process within BP, binding (22.5%) and catalytic […]

Pipeline specifications

Software tools Trinity, Bowtie, Corset, RAPSearch, TRAPID, MapMan