TABLE 1 .

Transcriptome sequencing read statistics, read processing, mapping, and coverage

Data set statistic	cEper1 in E. suzannae by sex and replicate
	Female			Male
	1st	2nd	3rd	1st	2nd	3rd
Total no. of reads	80,080,835	73,121,816	66,679,042	63,836,426	81,372,753	79,474,970
Trimmed reads, no. (%)	77,353,052 (96.59)	70,355,505 (96.22)	64,410,445 (96.60)	61,843,438 (96.88)	78,712,070 (96.73)	76,899,760 (96.76)
Trimmed reads mapped to C. hertigii cEper1 chromosome (genome size, 0.89 Mb), no. (%)	725,968 (0.94)	834,050 (1.19)	693,560 (1.08)	534,524 (0.86)	728,725 (0.93)	651,504 (0.85)
mRNA reads mapped    to chromosomal    genes, no. (%)	434,696 (59.87)	577,310 (69.21)	432,106 (62.30)	297,994 (55.75)	474,008 (65.05)	411,779 (63.20)
Reads assigned    to genes involved    in host-cell    interactions,a no. (%)	10,353 (2.38)	13,943 (2.42)	9,728 (2.25)	8,406 (2.82)	13,506 (2.85)	12,816 (3.11)
Reads assigned    to transporter    genes, no. (%)	23,327 (5.37)	30,589 (5.30)	20,910 (4.84)	17,040 (5.72)	25,305 (5.34)	23,663 (5.75)
Reads assigned to    transposases, no. (%)	23,102 (5.31)	31,299 (5.42)	18,775 (4.34)	18,508 (6.21)	30,759 (6.49)	29,227 (7.10)
Theoretical redundancy    of coverage	24.5×	32.5×	24.4×	16.8×	26.7×	23.2×
Single perfect coverage    (C. hertigii cEper1    chromosome), %	94.32	95.87	86.32	92.48	95.39	94.65
Trimmed reads mapped to C. hertigii pCher plasmid (genome size, 0.06 Mb), no. (%)	52,626 (0.07)	61,874 (0.09)	31,325 (0.05)	40, 882 (0.07)	63,651 (0.08)	64,554 (0.08)
mRNA reads mapped    to plasmid    genes, no.	37,892	44,723	23,215	28,795	45,146	44,688
Theoretical redundancy    of coverage	32.8×	38.7×	20.1×	24.9×	39.1×	38.7×
Single perfect coverage    (C. hertigii pCher    plasmid), %	88.69	91.38	73.19	86.51	91.15	90.49

^aIncluding ankyrin repeats, TPRs, and ubiquitin system-interacting genes.