The fosmid reads were mapped to the genome assembly using BLAT54.
We assessed the completeness of the genome assembly using BUSCO58 (version 3.0.2, Insecta dataset (1658 orthologues)).
Protein sequences were aligned to the assembly using GenBlastA (version 1.0.4 70.
The clean reads were then mapped to the Cq_real_v1.0 assembly using subread-align (v1.5.1 58.
Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
The assembly is a draft assembly using next generations sequencing reads and requires caution in usage.
These rRNA sequences were mapped to G. soja W05 genome assembly using BLAST44 (version 2.2.31) with default parameters.
High quality reads were pooled and used for the de novo assembly using Trinity v2.1.1 (ref. 18).
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Adaptor sequences were trimmed and reads were processed for de novo assembly using Velvet 1.0.1876 and then Oases 0.1.1877.
RNA-seq data were mapped to the assembly using Tophat (http://ccb.jhu.edu/software/tophat/index.shtml, version 2.0.8).
