Comprehensive Gene Annotation of the San Clemente Goat Genome

We employed EVidence Modeler (EVM)^{63 (link)} to consolidate RNA-seq, cDNA, and protein alignments with ab initio gene predictions and the CHIR_1.0 annotation into a final gene set. RNA-seq data included 6 tissues (hippocampus, hypothalamus, pituitary, pineal, testis, and thyroid) extracted from the domesticated San Clemente goat reference animal and 13 tissues pulled from NCBI SRA (Supplementary Table 11). Reads were cleaned with Trimmomatic^{64 (link)} and aligned to the genome with Tophat2^{65 (link)}. Alignments were then assembled independently with StringTie^{66 (link)}, Cufflinks^{67 (link)} and de novo assembled with Trinity^{68 (link)}. RNA-seq assemblies were combined and further refined using PASA^{63 (link)}. Protein and cDNA alignments using exonerate and tblastn with Ensembl datasets of Ovis aries, Bos taurus, Equus caballus, Sus scrofa, and Homo sapiens as well as NCBI annotation of Capra hircus and Ab initio predictions by Braker1^{69 (link)} were computed. The CHIR_1.0 annotation coordinates were translated into our coordinate system with the UCSC liftOver tool. All lines of evidence were then fed into EVM using intuitive weighting (RNAseq > cDNA/protein > ab initio gene predictions). Finally, EVM models were updated with PASA.