Pangenome analysis for 5 newly isolated strains and 35 publicly available M. avium subsp. paratuberculosis genomes. A The gene distribution of pangenome. The pangenome is divided into core, accessory, and unique genomes. B Each genome is classified into 24 COG categories; J: translation, ribosomal structure and biogenesis, A: RNA processing and modification, K: transcription, L: replication, recombination and repair, B: chromatin structure and dynamics, D: cell cycle control, cell division, chromosome partitioning, V: defense mechanisms, T: signal transduction mechanisms, M: cell wall/membrane/envelope biogenesis, N: cell motility, W: extracellular structures, U: intracellular trafficking, secretion, and vesicular transport, O: posttranslational modification, protein turnover, chaperones, X: mobilome: prophages, transposons, C: energy production and conversion, G: carbohydrate transport and metabolism, E: amino acid transport and metabolism, F: nucleotide transport and metabolism, H: coenzyme transport and metabolism, I: lipid transport and metabolism, P: inorganic ion transport and metabolism, Q: secondary metabolite biosynthesis, transport and catabolism, R: general function prediction, S: function.