Figure 2

Assessment of annotations. A) We benchmarked the MSA pipeline using Ensembl RheMac2 reference transcripts. We annotated 98.4% of the transcripts in RheMac2. 67.6% had unique annotation, matching the assigned gene in the database. The remaining 28.7% of the transcripts were not unambiguously matched due to mis-annotation in Ensembl or inconsistent naming conventions. MMU refers to species-specific Macaca mulatta transcripts; MIR refers to microRNA; LOCUS refers to Ensembl identifiers without a gene symbol. B) We evaluated the quality of annotations by comparing the gene expression profiles among Chlorocebus aethiops (AG), Macaca fascicularis (CM), Gorilla gorilla (GG), Homo sapiens (HS), Pan troglodytes (PT), and Rhesus macaque (RM). We performed principal component analysis on the expression of 6,463 orthologous genes in multiple tissues. We grouped together lymph node, marrow, and spleen (LMS), as they comprise the lymphatic system. The first two components explained 36.23% of the variance in the data, indicating the consistency of the CM and AG transcriptomes on a biological level.