Gene annotation, orthogroups and gene trees in Musa acuminata subspecies

Gene annotation was performed on the obtained de novo assembly for ‘Banksii’, ‘Maia Oa’ and ‘Calcutta 4,’ as well as on the draft Musa balbisiana ‘PKW’ assembly. Gene families were identified using OrthoFinder v1.1.4 with default parameters based on BLASTp (e-value 1e-5). Single-copy OGs (i.e. orthogroups with one copy of a gene in each of the five genotypes) from protein, coding DNA sequence (CDS), and genes (including introns and UTRs) were aligned with MAFFT v7.271 (Katoh & Standley 2013), and gene trees were constructed using PhyML v3.1 (Guindon et al. 2009) with ALrT branch support. All trees were rooted using Musa balbisiana as outgroup using Newick utilities v1.6 (Junier & Zdobnov 2010).