Differentially expressed transcripts of Tetracapsuloides bryosalmonae (Cnidaria) between carrier and dead-end hosts involved in key biological processes: novel insights from a coupled approach of FACS and RNA sequencing

Table 1 Summary of mapping data of FACS sorted Tetracapsuloides bryosalmonae

Samples	Number of raw reads	Number of quality-filtered reads	Number of reads mapping to brown trout or rainbow trout	Remaining: number of unmapped reads	Mapping of unmapped reads: number of mapping reads to different references
Samples	Number of raw reads	Number of quality-filtered reads	Number of reads mapping to brown trout or rainbow trout	Remaining: number of unmapped reads	E. leei mitochondrial genome (5 genes) GCA_001455295.2	K. iwatai mitochondrial genome (10 genes) GCA_001407235.2	M. squamalis (5710 genes) GCA_010108815.1	H. salminicola (8187 genes) GCA_009887335.1	S. zaharoni (number annotated genes) GCA_001455285.1	T. kitauei (15 020 genes) GCA_000827895.1	Combined T. bryosalmonae transcriptome (31 464 contigs, Ahmad et al. [20]; Faber et al. [19]; Kumar et al. [18]
BT_SC1	71 360 140	68 363 654	43 666 912	24 696 742	2 308 164	3 837 812	2 121 654	2 121 654	2 383 909	3 297 048	13 551 795
BT_SC2	76 160 696	73 576 346	44 245 459	29 330 887	2 936 500	4 862 586	2 656 946	2 656 946	3 017 066	4 109 527	16 276 440
BT_SC3	80 297 000	76 804 534	48 592 048	28 212 486	2 495 135	4 166 910	2 332 754	2 332 754	2 576 958	3 586 536	15 870 805
RT_SC1	59 057 686	56 787 460	37 180 648	19 606 812	1 991 590	3 036 937	1 659 712	1 659 712	1 859 904	2 641 455	8 123 191
RT_SC2	87 380 018	83 725 584	51 212 973	32 512 611	3 551 579	5 591 392	2 989 800	2 989 800	3 505 367	4 802 022	14 838 808
RT_SC3	72 073 626	68 923 366	48 272 618	20 650 748	1 801 703	2 812 857	1 467 204	1 467 204	1 770 479	2 411 495	7 777 966

The filtered clean reads of sorted T. bryosalmonae obtained from infected kidney of brown trout and rainbow trout were mapped to different genome and transcriptome references (fish hosts and myxozoan parasites). The remaining unmapped reads were mapped against the genomes of different myxozoan parasites and the combined transcriptome of T. bryosalmonae from brown trout, rainbow trout and bryozoan hosts. RNA-seq analysis was performed using CLC Genomics Workbench software version 22. T. bryosalmonae samples from brown trout: BT_SC1, BT_SC2, BT_SC3; T. bryosalmonae samples from rainbow trout: RT_SC1, RT_SC2, RT_SC3.

ISSN: 1297-9716