Table 1. Sequencing Metrics of the 10 RNA-seq Libraries.

Source	Library	Total Paired Reads	Mapping to T. cacao	Mapping to M. perniciosa
Infected plants	I1	77,308,238	56,884,442 (73.58%)	265,238 (0.34%)
	I2	207,441,756	167,016,562 (80.51%)	904,727 (0.44%)
	I3	83,953,292	67,870,238 (80.84%)	196,086 (0.23%)
	I4	90,591,723	71,473,561 (78.90%)	186,831 (0.21%)
	I5	103,196,353	82,127,996 (79.58%)	158,021 (0.15%)
	Total	562,491,362	445,372,799 (79.18%)	1,710,903 (0.30%)
Healthy plants	H1	89,659,731	73,930,327 (82.46%)	27 (0.00%)
	H2	82,560,659	68,560,121 (83.04%)	633 (0.00%)
	H3	86,454,964	68,962,874 (79.77%)	208 (0.00%)
	H4	80,950,589	65,521,727 (80.94%)	91 (0.00%)
	H5	96,856,054	73,928,395 (76.33%)	12 (0.00%)
	Total	436,481,997	350,903,444 (80.39%)	971 (0.00%)