title: RNA-seq  of Trypanosoma evansi: 4V1M clone group
design: RNA-seq data were generated using the Illumina HiSeq 4000 system. After data filtering, the clean reads were assembled by Trinity (v2.0.6). Blast v2.2.25 (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for aligning unigenes to the databases of Nt, Nr, COG, KEGG, and SwissProt for annotation; Blast2GO v2.5.0 (https://www.blast2go.com) was utilized with NR annotation to obtain gene ontology (GO) annotation; and InterProScan5 v5.17-56.0 (https://code.google.com/p/interproscan/wiki/Introduction) was employed for InterPro annotation. For predicting the coding sequence (CDS) of unigenes, we selected the segments of the unigenes that best mapped to functional databases in the priority order of NR, SwissProt, KEGG, and COG. The CDS of unigenes that could not be aligned to any of these database were predicted by ESTScan v3.0.2 (http://sourceforge.net/projects/estscan) using a Blast-predicted CDS model. TFs were predicted using the getorf feature of EMBOSS 6.5.7 (http://genome.csdb.cn/cgi-bin/emboss/help/getorf), which was then aligned to TF domains with HMMER v3.1b2 (http://hmmer.org). Unigene single sequence repeats (SSRs) were detected by MISA v1.0 (http://pgrc.ipk-gatersleben.de/misa), and primers for each SSR were designed with Primer 3 v2.3.7 (http://bioinfo.ut.ee/primer3). All clean reads were mapped to unigenes using HISAT v0.1.6-beta. Next, SNPs were identified with GATK v3.4-0.